Re: [gmx-users] topology file of ligand
On 10/15/13 11:24 AM, sunyeping wrote: Dear gromacs users, I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he immediately notice three things that are wrong with this topology, which include charge group, H atom charge, etc. And the author then reconstructed a topology file. I don't understand how the charge group and charge of individual atom are correctly assigned. Could you explain it to me? The Gromos96 parameter sets assign charges and charge groups based on chemical functional groups that are transferable between molecules. Spotting inaccuracies and knowing how to fix them come with understanding how the force field was derived (read the primary literature and study existing molecules). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology and coordinate file not matching after grompp
On 7/31/13 6:04 AM, chinnu657 wrote: Hello, I have a problem and although I've read almost everything the internet could offer on how differently people have approached this problem, mine hasn't been solved yet. Basically, I am trying to mix 2 different proteins in one box and after doing my grompp to neutralise the system, I get the error number of coordinates in coordinate file (solvated.gro, 85059) does not match topology (topol.top, 85079). This is how my topology file looks: ;GROMACS toplogy ; ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #include topol_2CDS.itp ;Include water topology #include spce.itp ;Include generic ion topology #include ions.itp [ system ] Two proteins in water [ molecules ] Protein_1AKI1 Protein_2CDS1 SOL 27053 How can I deduce from this data that the number of coordinates in topol.top is 85079. And what exactly should I do to reduce the number of molecules here so that the 2 files have the same number of coordinates. Number of atoms in Protein_1AKI [moleculetype] + number of atoms in Protein_2CDS [moleculetype] + (3*27053) is the number of atoms that the topology specifies. Cross-check that against the coordinate file. This error always arises for the same reason - incorrect bookkeeping of some sort. You haven't said how you built the system or what commands you gave, for instance, to genbox, so it's hard to be more specific. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology file-residue unknown
On Sat, Apr 6, 2013 at 5:56 AM, Juliette N. joojoojo...@gmail.com wrote: Thank you Justin. I have now the topology. I have a quick question regarding atom types. I used opls_143 and opls_144 for C and H of ethylene respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe these are not the proper atomtypes for H2C=CH2. http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds Mark rtp entry: [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 From atomtypes.atp opls_141 12.01100 ; alkene C (R2-C=) opls_142 12.01100 ; alkene C (RH-C=) * opls_143 12.01100 ; alkene C (H2-C=) opls_1441.00800 ; alkene H (H-C=)* Did I select the correct atomtypes? Thanks many times! On 4 April 2013 18:23, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 6:17 PM, Juliette N. wrote: Hi Justin, Thanks a lot for your message. I am petrified why pdb2gmx is not recognizing the residue ETY. This the first residue added to ffoplsaa.rtp but as you may see below it is not read from rtp. I am sure this residue is added to ffoplsaa.rtp which is existing in the working directory: [ ETY ] [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 ;C2C1 Then I issue: pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.5.4 (-: Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**watermodels.dat Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 6 Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.r2b Reading Ethylene.gro... Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 No occupancies in Ethylene.gro Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.hdb Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.c.tdb Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1# Processing chain 1 (6 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --**- Program pdb2gmx, VERSION 4.5.4 Source code file: resall.c, line: 581 Fatal error: Residue 'ETY' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errors http://www.gromacs.org/Documentation/Errors I am kind of baffled what could be wrong. I would really appreciate if you could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I doubt)? Do i have to edit esiduetypes.dat? You've added the .rtp entry incorrectly. pdb2gmx in version 4.5 and above needs .rtp files to be organized in force field subdirectories (in your case oplsaa.ff). It will not recognize a file called ffoplsaa.rtp, which is the pre-4.5 syntax for force field files. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
Re: [gmx-users] Topology file-residue unknown
Thank you Justin. I have now the topology. I have a quick question regarding atom types. I used opls_143 and opls_144 for C and H of ethylene respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe these are not the proper atomtypes for H2C=CH2. rtp entry: [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 From atomtypes.atp opls_141 12.01100 ; alkene C (R2-C=) opls_142 12.01100 ; alkene C (RH-C=) * opls_143 12.01100 ; alkene C (H2-C=) opls_1441.00800 ; alkene H (H-C=)* Did I select the correct atomtypes? Thanks many times! On 4 April 2013 18:23, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 6:17 PM, Juliette N. wrote: Hi Justin, Thanks a lot for your message. I am petrified why pdb2gmx is not recognizing the residue ETY. This the first residue added to ffoplsaa.rtp but as you may see below it is not read from rtp. I am sure this residue is added to ffoplsaa.rtp which is existing in the working directory: [ ETY ] [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 ;C2C1 Then I issue: pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.5.4 (-: Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**watermodels.dat Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 6 Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.r2b Reading Ethylene.gro... Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 No occupancies in Ethylene.gro Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.hdb Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.c.tdb Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1# Processing chain 1 (6 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --**- Program pdb2gmx, VERSION 4.5.4 Source code file: resall.c, line: 581 Fatal error: Residue 'ETY' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors I am kind of baffled what could be wrong. I would really appreciate if you could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I doubt)? Do i have to edit esiduetypes.dat? You've added the .rtp entry incorrectly. pdb2gmx in version 4.5 and above needs .rtp files to be organized in force field subdirectories (in your case oplsaa.ff). It will not recognize a file called ffoplsaa.rtp, which is the pre-4.5 syntax for force field files. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**
Re: [gmx-users] Topology file-residue unknown
On 4/4/13 11:38 AM, Juliette N. wrote: Dear all, I am having trouble creating topology file for simple molecule ethylene. Here is the steps. Below is the pdb file: Ethylene.pdb: ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00 C ATOM 2 C2 ETY 1 -0.672 -0.000 0.000 1.00 0.00 C ATOM 3 H11 ETY 1 1.238 -0.928 0.000 1.00 0.00 H ATOM 4 H12 ETY 1 1.238 0.928 0.000 1.00 0.00 H ATOM 5 H21 ETY 1 -1.238 -0.928 0.000 1.00 0.00 H ATOM 6 H22 ETY 1 -1.238 0.928 0.000 1.00 0.00 H END Then: editconf -f Ethylene.pdb -o Ethylene.gro Ethylene.gro: 6 1ETY C11 0.067 -0.000 0.000 1ETY C22 -0.067 -0.000 0.000 1ETYH113 0.124 -0.093 0.000 1ETYH124 0.124 0.093 0.000 1ETYH215 -0.124 -0.093 0.000 1ETYH226 -0.124 0.093 0.000 0.0 0.0 0.0 Then I add the following residue for ethylene to the rtp file ffoplsaa.rtp: [ ETY ] [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 C2C1 C1 C2 and C2 C1 are redundant. You don't need both. and then ; pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa Q1_ i dont realize what is the difference between the already created Ethylene.gro and the one in the pdb2gmx(GRO.gro). I am not getting the latter and was wondering what would be the diffrence? pdb2gmx produces an output coordinate file as a byproduct of its massively complicated fix-build-process procedure. If you're not getting the output file(s), then pdb2gmx is failing and should produce obvious error messages. Q2) Below is the top file which is not generated. Once I Issue pdb2gmx, I enter 6 because pdb2gmx output says: Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermo$ 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoac$ No occupancies in Ethylene.gro Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtyp$ And finally I get a blank top file:: ;File 'Ethylene.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.4 ; ;Command line was: ;pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa ; ;Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp - output says: Select the Water Model: Reading Ethylene.gro... Read 'GROningen Mixture of Alchemy and Childrens' Stories', 6 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 Reading residue database... (oplsaa) Processing chain 1 (6 atoms, 1 residues) Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. There should be more output after this line. Any reason for pdb2gmx to fail would be printed here. Is there something wrong with my rtp? Could I trouble you to let me know what wrong is? I can see nothing wrong. I was able to produce a sensible topology using all of your input files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology file-residue unknown
Hi Justin, Thanks a lot for your message. I am petrified why pdb2gmx is not recognizing the residue ETY. This the first residue added to ffoplsaa.rtp but as you may see below it is not read from rtp. I am sure this residue is added to ffoplsaa.rtp which is existing in the working directory: [ ETY ] [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 ;C2C1 Then I issue: pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.5.4 (-: Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 6 Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading Ethylene.gro... Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 No occupancies in Ethylene.gro Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1# Processing chain 1 (6 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.4 Source code file: resall.c, line: 581 Fatal error: Residue 'ETY' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am kind of baffled what could be wrong. I would really appreciate if you could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I doubt)? Do i have to edit esiduetypes.dat? Thank you many times for your precious time, On 4 April 2013 17:21, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 11:38 AM, Juliette N. wrote: Dear all, I am having trouble creating topology file for simple molecule ethylene. Here is the steps. Below is the pdb file: Ethylene.pdb: ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00 C ATOM 2 C2 ETY 1 -0.672 -0.000 0.000 1.00 0.00 C ATOM 3 H11 ETY 1 1.238 -0.928 0.000 1.00 0.00 H ATOM 4 H12 ETY 1 1.238 0.928 0.000 1.00 0.00 H ATOM 5 H21 ETY 1 -1.238 -0.928 0.000 1.00 0.00 H ATOM 6 H22 ETY 1 -1.238 0.928 0.000 1.00 0.00 H END Then: editconf -f Ethylene.pdb -o Ethylene.gro Ethylene.gro: 6 1ETY C11 0.067 -0.000 0.000 1ETY C22 -0.067 -0.000 0.000 1ETYH113 0.124 -0.093 0.000 1ETYH124 0.124 0.093 0.000 1ETYH215 -0.124 -0.093 0.000 1ETYH226 -0.124 0.093 0.000 0.0 0.0 0.0 Then I add the following residue for ethylene to the rtp file ffoplsaa.rtp: [ ETY ] [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 C2C1 C1 C2 and C2 C1 are redundant. You don't need both. and then ; pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa Q1_ i dont realize what is the difference between the already created Ethylene.gro and the one in the pdb2gmx(GRO.gro). I am not getting the latter and was wondering what would be the diffrence? pdb2gmx
Re: [gmx-users] Topology file-residue unknown
On 4/4/13 6:17 PM, Juliette N. wrote: Hi Justin, Thanks a lot for your message. I am petrified why pdb2gmx is not recognizing the residue ETY. This the first residue added to ffoplsaa.rtp but as you may see below it is not read from rtp. I am sure this residue is added to ffoplsaa.rtp which is existing in the working directory: [ ETY ] [ atoms ] C1opls_143-0.1201 H11 opls_144 0.0601 H12 opls_144 0.0601 C2opls_143-0.1202 H21 opls_144 0.0602 H22 opls_144 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 ;C2C1 Then I issue: pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.5.4 (-: Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 6 Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading Ethylene.gro... Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 No occupancies in Ethylene.gro Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1# Processing chain 1 (6 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.4 Source code file: resall.c, line: 581 Fatal error: Residue 'ETY' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am kind of baffled what could be wrong. I would really appreciate if you could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I doubt)? Do i have to edit esiduetypes.dat? You've added the .rtp entry incorrectly. pdb2gmx in version 4.5 and above needs .rtp files to be organized in force field subdirectories (in your case oplsaa.ff). It will not recognize a file called ffoplsaa.rtp, which is the pre-4.5 syntax for force field files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology
On 3/18/13 10:39 AM, shahid nayeem wrote: Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one of the CYS, SH in the form of SG as if it is involved in disulfide linkage, while the other chain with which I expect it to form disulfide link is not in the input pdb file. or can I use pdb2gmx command and get the separate .top and .gro file for each chain using index file. You may be able to use the -cys option to fool pdb2gmx, but I don't know if that will cause problems. Having half a disulfide present is odd, though some force fields support thiolate or neutral (i.e. radical) forms of cysteine. You'll have to look into the force field files to see what's available. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology
I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx. shahid On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 10:39 AM, shahid nayeem wrote: Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one of the CYS, SH in the form of SG as if it is involved in disulfide linkage, while the other chain with which I expect it to form disulfide link is not in the input pdb file. or can I use pdb2gmx command and get the separate .top and .gro file for each chain using index file. You may be able to use the -cys option to fool pdb2gmx, but I don't know if that will cause problems. Having half a disulfide present is odd, though some force fields support thiolate or neutral (i.e. radical) forms of cysteine. You'll have to look into the force field files to see what's available. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology
On 3/18/13 10:49 PM, shahid nayeem wrote: I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx. shahid My apologies. For some reason I always think there is a -cys option, when in fact it is -ss. In any case, if you're trying to treat some strange form of cysteine, some force fields have special names for different forms (CYM for thiolate, etc) so naming and proper force field choice may be the only viable mechanism here. -Justin On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 10:39 AM, shahid nayeem wrote: Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one of the CYS, SH in the form of SG as if it is involved in disulfide linkage, while the other chain with which I expect it to form disulfide link is not in the input pdb file. or can I use pdb2gmx command and get the separate .top and .gro file for each chain using index file. You may be able to use the -cys option to fool pdb2gmx, but I don't know if that will cause problems. Having half a disulfide present is odd, though some force fields support thiolate or neutral (i.e. radical) forms of cysteine. You'll have to look into the force field files to see what's available. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology of Graphite Oxide
On 3/7/13 3:36 AM, zhhxu wrote: Hi users: I want to run a simulation of adsorption of protein on graphite oxide(GO) which is oxidized at random and is near 80% coverage by hydroxyl and epoxyl group. My first question is how to generate a topology filefor GO. Previous to search solution to this problem in this forum, I had tried to make a topology for GO use g_x2top with command: g_x2top -f input.pdb -nopbc -r outputname -o outputname. But g_x2top did not work fine(fine for prestine graphite) and gave error messages like Can not find forcefield for atom .. The .n2t files provided with the (few) force fields in Gromacs are rather inflexible, so you will probably need to modify them to suit your needs. My second also is about definition of improper dihedral in opls-aa. Whether it is validate to assign a improper dihedral for a central sp2 carbon atom with three other bonded atoms no matter of what is type of other three atom? I have gotten (mentioned above) a topology file of pristine graphite for opls-aa with g_x2top(the command is similar to above), but the topology file did not include any improper dihedral. g_x2top doesn't write impropers, so you have to manually add them if needed. Assignment of proper parameters should be done based on analogous functional groups present in the force field or by a suitable derivation protocol. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR
On 9/16/12 10:45 PM, Sonia Milena Aguilera Segura wrote: Hi, I'm preparing my mdp and topology files for running free energy calculations using BAR method. I´m using Justin Lemkul's tutorial as a reference (You can find it here http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html). According to this tutorial, the simultaneous coupling of both Coulombic and van der Waals terms leads to instability. So, it is usefull to prepare the mdp files as follows (off course including all other parameters): van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= LIG couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= LIG couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B However, I don't understand how can this leads to a fully interacting molecule if all the charges in the topology file have been set to zero. Does it mean that for the second calculation (coulombic coupling) I have to use the original topology file with all charges? Or, should I use the same topology with zero charges? You do not need to make any changes to the topology. The couple-lambda* settings dictate which parameters are involved in the calculations. In the second examples, in the lambda=0 state, only van der Waals interactions are calculated, but when lambda=1, both van der Waals and Coulombic interactions (vdw-q) are calculated. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology generated of a dimer protein
On 9/9/12 8:42 AM, Shima Arasteh wrote: Hi all, I am simulating a system of protein and water. My protein is composed of 2 monomers, each monomer has its own C- and N-terminus, so there are 2 N-terminals and 2 C-terminals. I have a pdb of two monomers as dimer.pdb. I tried to generate topology of dimer.pdb. But 2 monomers are identified as one fragment which has one -N-terminus and one C-terminus! So the generated topology file and the total charge would be incorrect. How can I solve it? Any suggestions please? The chains need to be either separated by a TER entry or have different chain identifiers. pdb2gmx uses the -chainsep option to control the criteria for a new chain, and by default it uses either of these. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology- make bonds with certain cut-off distance
Hi, In case you want the bonds to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing. Erik 25 aug 2012 kl. 06.54 skrev mohan maruthi sena: Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, Thanks in advance, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology- make bonds with certain cut-off distance
Hi , Thanks for your reply. I actually want to build an elastic network model (ENM) for Protein containing 372 residues. According to literature, ENM model only considers C-alpha atoms of protein and discards rest of the atoms.The potential only considers bonded term only. It does not contain angle,dihedral or non-bonded term. To build an ENM model the specified atom makes bond with all other atoms with certain cutoff distance. I consider the distance between two c-alpha atoms is 0.38nm and force constant of 69.1 kj/(nm)2.I have written a code which gives the number of atoms around a particular atom with in certain cut-off distance, With this i will know what are the atoms that are needed to connect a particular atom.I have generated .gro and .top files using pdb2gmx command . After generating topology file , I replace bonds section with the connectivity information i get from code. The next steps are equilibration and production. I am not sure whether it takes connectivity information from topology or not. If it is not then how can i mention it forms bonds with in certain distance . Finally , if i run the simulation with all the above mentioned steps and load the trajectory in vmd , the protien gets contracted after first step. Thanks, Mohan On Sat, Aug 25, 2012 at 3:43 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, In case you want the bonds to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing. Erik 25 aug 2012 kl. 06.54 skrev mohan maruthi sena: Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, Thanks in advance, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology file for simulation of inorganic compounds
On 8/13/12 1:49 PM, Deepak Ojha wrote: Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. Likely you will have to do it manually, which means you will have to understand Chapter 5 of the manual and the proper parameterization protocol for your molecules under the chosen force field. Some web servers exist for such purposes, depending on the force field you want to use. Otherwise consult the following page and be prepared for a significant time investment: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology file for simulation of inorganic compounds
On 2012-08-13 21:39, Justin Lemkul wrote: On 8/13/12 1:49 PM, Deepak Ojha wrote: Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. Likely you will have to do it manually, which means you will have to understand Chapter 5 of the manual and the proper parameterization protocol for your molecules under the chosen force field. Some web servers exist for such purposes, depending on the force field you want to use. Otherwise consult the following page and be prepared for a significant time investment: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Hm, that page is slightly outdated. You want to google for antechamber / gaff /amber respectively charmm / cgenff -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology file
On 2012-07-26 22:09, Shima Arasteh wrote: Hi all, To check a topology, is it correct to compare topologies generated by 2 different force fields? For example with gmx and charmm36. I know the topology generated by gmx is correct, however the parameters might be different. You can not compare directly in this way, since different force field may have different number of e.g. dihedral terms. Never use the gmx force field by the way. Thanks in advance . Sincerely, Shima -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file in DPPC
On 5/15/12 10:47 AM, scapr...@uniroma3.it wrote: Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that I should change my topology file but I'm not able to find within my topology file (obtained by using pdb2gmx on my protein) #includegromos53a6.ff/forcefield.itpstatement so as to replace this line with #include gromos53a6_lipid.ff/forcefield.itp, as reported in the tutorial. Indeed, at the top of my topology file I have got; ; Include forcefield parameters #include ffG53a6.itp and, after the list of all atoms, at the bottom of the file; ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name PHOSPHOLIPASE A2, AMMODYTOXIN A [ molecules ] ; Compound#mols Protein_A 1 I'm wondering if it may depend on the fact I have got the version gromacs-4.0.7 and not the version 4.5.3 or newer or if I have to change some options when I launch the command pdb2gmx in order to build my topology file. I used the following command: pdb2gmx -f 3G8G.pdb -o 3G8G_membr.gro -p 3G8G_membr.top -i 3G8G_membr.itp -ignh -water spc and I chose GROMOS96 53A6 Please, let me know. The problem is you're using an old version. The tutorial states that you are expected to be using a version in the 4.5.x series. If you don't, then the procedure will be somewhat different. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file in DPPC
Do you know where I should look to find the solution to my problem? Silvia On 5/15/12 10:47 AM, scapr...@uniroma3.it wrote: Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that I should change my topology file but I'm not able to find within my topology file (obtained by using pdb2gmx on my protein) #includegromos53a6.ff/forcefield.itpstatement so as to replace this line with #include gromos53a6_lipid.ff/forcefield.itp, as reported in the tutorial. Indeed, at the top of my topology file I have got; ; Include forcefield parameters #include ffG53a6.itp and, after the list of all atoms, at the bottom of the file; ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name PHOSPHOLIPASE A2, AMMODYTOXIN A [ molecules ] ; Compound#mols Protein_A 1 I'm wondering if it may depend on the fact I have got the version gromacs-4.0.7 and not the version 4.5.3 or newer or if I have to change some options when I launch the command pdb2gmx in order to build my topology file. I used the following command: pdb2gmx -f 3G8G.pdb -o 3G8G_membr.gro -p 3G8G_membr.top -i 3G8G_membr.itp -ignh -water spc and I chose GROMOS96 53A6 Please, let me know. The problem is you're using an old version. The tutorial states that you are expected to be using a version in the 4.5.x series. If you don't, then the procedure will be somewhat different. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file in DPPC
On 5/15/12 11:11 AM, scapr...@uniroma3.it wrote: Do you know where I should look to find the solution to my problem? The entire procedure for modifying the force field is different, as the directory structure and file names are very different. The best solution is to upgrade your Gromacs version and follow the tutorial directly. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology parameters
IS the parameters for a residue in CHARMM36 and CHARMM27 the same? Thanks in advance, Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, May 5, 2012 9:16 PM Subject: Re: [gmx-users] Topology parameters On 5/5/12 11:39 AM, Shima Arasteh wrote: Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27? Maybe, try it and see. Swiss-Param might also be an option. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology parameters
On 5/6/12 2:36 PM, Shima Arasteh wrote: IS the parameters for a residue in CHARMM36 and CHARMM27 the same? I would suggest you do a bit of reading about the CHARMM force field hierarchy and why they are named as they are. If you're parameterizing a new residue you can do it for either, or both, depending on the parameter set. In your case, I'd suspect your formyl parameters are going to be universal between CHARMM27 and CHARMM36, but don't let my suggestion be your justification. If a reviewer asks, some guy on the Internet said it is not sufficient justification ;) -Justin Thanks in advance, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, May 5, 2012 9:16 PM *Subject:* Re: [gmx-users] Topology parameters On 5/5/12 11:39 AM, Shima Arasteh wrote: Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27? Maybe, try it and see. Swiss-Param might also be an option. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology parameters
All right. Thank you so much. Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 6, 2012 11:32 PM Subject: Re: [gmx-users] Topology parameters On 5/6/12 2:36 PM, Shima Arasteh wrote: IS the parameters for a residue in CHARMM36 and CHARMM27 the same? I would suggest you do a bit of reading about the CHARMM force field hierarchy and why they are named as they are. If you're parameterizing a new residue you can do it for either, or both, depending on the parameter set. In your case, I'd suspect your formyl parameters are going to be universal between CHARMM27 and CHARMM36, but don't let my suggestion be your justification. If a reviewer asks, some guy on the Internet said it is not sufficient justification ;) -Justin Thanks in advance, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, May 5, 2012 9:16 PM *Subject:* Re: [gmx-users] Topology parameters On 5/5/12 11:39 AM, Shima Arasteh wrote: Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27? Maybe, try it and see. Swiss-Param might also be an option. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology parameters
On 5/5/12 9:21 AM, Shima Arasteh wrote: Dear gmx users, I need to define a new residue topology ( Formyl ) in CHARMM27 force field. I have the formyl parameters for GROMOS. I'd like to know if the residue parameters are the same in different force fields? Almost certainly not. Each force field has different parameterization procedures and makes use of different atom types. A new force field requires a new topology. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology parameters
Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27? Cheers, Shima From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, May 5, 2012 5:58 PM Subject: Re: [gmx-users] Topology parameters On 5/5/12 9:21 AM, Shima Arasteh wrote: Dear gmx users, I need to define a new residue topology ( Formyl ) in CHARMM27 force field. I have the formyl parameters for GROMOS. I'd like to know if the residue parameters are the same in different force fields? Almost certainly not. Each force field has different parameterization procedures and makes use of different atom types. A new force field requires a new topology. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology parameters
On 5/5/12 11:39 AM, Shima Arasteh wrote: Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27? Maybe, try it and see. Swiss-Param might also be an option. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology files
kirtana S wrote: Dear Users, In the gromacs manual on means to convert the pdb file to gromacs topology file I need to use pdb2gmx. Here I have to specify the force field .How to work with organic residues which do not exists . Since I had used general amber force field, and could not find this in the /share/top/ directory . Do I need to manually construct the .itp file for each residues. What will be the easiest way to construct a solvated box with user defined residues in gromacs. If the residue of interest will be a component of a polymeric molecule like a protein, refer to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field. If the molecule is a standalone species like a ligand, solvent, etc then all you have to do is #include an .itp file in the system topology. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology files
For example if I have a polystyrene polymer chains and monomers of user defined solvent . I need to construct the .itp file by hand . Thanks for the reply Kirtana On Tue, Feb 28, 2012 at 5:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: kirtana S wrote: Dear Users, In the gromacs manual on means to convert the pdb file to gromacs topology file I need to use pdb2gmx. Here I have to specify the force field .How to work with organic residues which do not exists . Since I had used general amber force field, and could not find this in the /share/top/ directory . Do I need to manually construct the .itp file for each residues. What will be the easiest way to construct a solvated box with user defined residues in gromacs. If the residue of interest will be a component of a polymeric molecule like a protein, refer to http://www.gromacs.org/** Documentation/How-tos/Adding_**a_Residue_to_a_Force_Fieldhttp://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field. If the molecule is a standalone species like a ligand, solvent, etc then all you have to do is #include an .itp file in the system topology. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology files
kirtana S wrote: For example if I have a polystyrene polymer chains and monomers of user defined solvent . I need to construct the .itp file by hand . Polystyrene is most easily generated using .rtp entries in pdb2gmx. The solvent can be described by manually created .itp files. http://www.gromacs.org/Documentation/How-tos/Polymers -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology files
kirtana S wrote: Thanks for the documentation. Again I have a ligand terminated silica nanoparticle ,what can be the easiest way to approach the topology file for this. I don't know what the structure is, but I'll assume the .rtp route is probably easier than writing a (presumably) repetitive topology for a relatively large particle. You may or may not need to invoke specbond.dat for cross-links, as pdb2gmx can deal only with linear species via .rtp entries; other bonds are introduced with specbond.dat. -Justin On Tue, Feb 28, 2012 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: kirtana S wrote: For example if I have a polystyrene polymer chains and monomers of user defined solvent . I need to construct the .itp file by hand . Polystyrene is most easily generated using .rtp entries in pdb2gmx. The solvent can be described by manually created .itp files. http://www.gromacs.org/__Documentation/How-tos/Polymers http://www.gromacs.org/Documentation/How-tos/Polymers -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology files
Thanks for the reply. As I am new to GROMACS I am not able to understand. I will go through the manual and will get back if I have further questions. On Tue, Feb 28, 2012 at 6:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: kirtana S wrote: Thanks for the documentation. Again I have a ligand terminated silica nanoparticle ,what can be the easiest way to approach the topology file for this. I don't know what the structure is, but I'll assume the .rtp route is probably easier than writing a (presumably) repetitive topology for a relatively large particle. You may or may not need to invoke specbond.dat for cross-links, as pdb2gmx can deal only with linear species via .rtp entries; other bonds are introduced with specbond.dat. -Justin On Tue, Feb 28, 2012 at 5:46 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: kirtana S wrote: For example if I have a polystyrene polymer chains and monomers of user defined solvent . I need to construct the .itp file by hand . Polystyrene is most easily generated using .rtp entries in pdb2gmx. The solvent can be described by manually created .itp files. http://www.gromacs.org/__**Documentation/How-tos/Polymershttp://www.gromacs.org/__Documentation/How-tos/Polymers http://www.gromacs.org/**Documentation/How-tos/Polymershttp://www.gromacs.org/Documentation/How-tos/Polymers ** -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology missing
On 25/01/2012 9:39 PM, Anik Sen wrote: Hi, I am using GROMACS 4.5.5. I made the pdb file of DNA and changed its residue files according to the given dna.rtp. But still am getting an error 'OH' residue topology file missing where as the 'OH' is present in the atomtype as well as the residue topology file. Whats the reason? Copy and paste the actual error message, along with your command line, and any of the other output that you think might be relevant. It's a waste of time to give help based on information filtered through someone's head, because you don't know when their error might have occurred (if any!). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology and parameter for cobalt metal
shahid nayeem wrote: Dear all I am interested in simulating a model protein with cobalt forming coordinate bond with His. I coud'nt find entry for cobalt in any forcefield .rtp file. I am using Gromacs 4.5.4 . If any one can help me in getting forcefield parameters for charmm27/ OPLSaa/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Standard, non-polarizable MM force fields are not particularly well-suited for dealing with transition metals. Fixed point charges on such species, especially those coordinated to amino acids, are generally very incorrect, not to mention geometric coordination parameters that are not built-in. http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology error
On 21/11/2011 9:18 PM, archana sonawani wrote: Dear Sir/Madam, For orienting the protein and membrane, I have used the .mdp and following topology file: ; ; File 'topol_popc.top' was generated ; By user: jalemkul (502) ; On host:bevany.biochem.vt.edu http://bevany.biochem.vt.edu ; At date: Fri Oct 20 13:26:53 2006 ; ; This is your topology file ; ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; Include ion topologies #include gromos53a6_lipid.ff/ions.itp ; System specifications [ system ] 60-Lipid POPC Bilayer [ molecules ] ; molecule name nr. POPC 60 SOL 1536 After running grompp to generate .tpr file I get following error: Program grompp, VERSION 4.5.4 Source code file: gmxcpp.c, line: 248 Fatal error: Topology include file gromos53a6_lipid.ff/forcefield.itp not found But in the above topology file, if I change the #include gromos53a6_lipid.ff/forcefield.itp line to *;*include gromos53a6_lipid.ff/forcefield.itp This file is not optional, so failing to include anything makes further problems. You need such a file. You are doing something non-standard, so your burden of following directions, and/or understanding how the include file and force field mechanism works is a bit higher than normal :-) Mark I get following error: Program grompp, VERSION 4.5.4 Source code file: topio.c, line: 653 Fatal error: Syntax error - File popc.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype Can anyone help me out...Thanks in adv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology dihedral or improper dihedral
On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com wrote: Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. Thank you very much!!! Best! Xueming -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology dihedral or improper dihedral
Thank you for your reply, Lina. I did try the prodrg server before. For A molecule, there is no improper dihedral. A just has one dihedral for the head group. For B molecule, it gives improper dihedral of the tetra nitrogen. I am wondering what is the criteria or at least a guidance of what could be the best choice for the topology file. Or any choices could be right and I have to try which one provide consistent results with experiment by trial? Best! Xueming On Sun, Nov 13, 2011 at 9:57 AM, lina lina.lastn...@gmail.com wrote: On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com wrote: Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. Thank you very much!!! Best! Xueming -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology dihedral or improper dihedral
XUEMING TANG wrote: Thank you for your reply, Lina. I did try the prodrg server before. For A molecule, there is no improper dihedral. A just has one dihedral for the head group. For B molecule, it gives improper dihedral of the tetra nitrogen. I am wondering what is the criteria or at least a guidance of what could be the best choice for the topology file. Or any choices could be right and I have to try which one provide consistent results with experiment by trial? I see no reason why a quaternary nitrogen would need an improper dihedral assigned to it. Some impropers in Gromos96 are applied to tetrahedral groups like alpha-carbons because there is no explicit H atom present, thus the stereochemistry is maintained with an improper so that the groups do not invert. With four explicit substituents, an improper should not be necessary. -Justin Best! Xueming On Sun, Nov 13, 2011 at 9:57 AM, lina lina.lastn...@gmail.com mailto:lina.lastn...@gmail.com wrote: On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com mailto:yujan2...@gmail.com wrote: Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. Thank you very much!!! Best! Xueming -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology for a new ligand
Kavyashree M wrote: Dear gromacs users, I wanted to know the steps to be followed in order to generate a topology for a new ligand. I went through the mailing list and http://www.gromacs.org/Documentation/How-tos/Parameterization but was not clear. All force fields are different, and since you haven't said which one you're trying to use there's nothing that anyone can tell you. Read the primary literature for the force field you want to use and follow the procedure laid out therein. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology for a new ligand
Dear users, I was mentioning about OPLSAA force field for ATP and other small molecule. I just wanted to know the procedure to be followed and some guidance from people who have created topologies for such molecules manually. I am going through chapter 5 of the manual. But wanted some useful suggestions. Thank you With Regards M. Kavyashree On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear gromacs users, I wanted to know the steps to be followed in order to generate a topology for a new ligand. I went through the mailing list and http://www.gromacs.org/**Documentation/How-tos/**Parameterizationhttp://www.gromacs.org/Documentation/How-tos/Parameterization but was not clear. All force fields are different, and since you haven't said which one you're trying to use there's nothing that anyone can tell you. Read the primary literature for the force field you want to use and follow the procedure laid out therein. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology for a new ligand
Kavyashree M wrote: Dear users, I was mentioning about OPLSAA force field for ATP and other small molecule. I just wanted to know the procedure to be followed and some guidance from people who have created topologies for such molecules manually. I am going through chapter 5 of the manual. But wanted some useful suggestions. Methods for parameterizing molecules for OPLS-AA are described in fairly extensive detail in the 2001 OPLS-AA paper cited in the manual. The manual itself will only tell you how to implement parameters in Gromacs, not how to derive them. -Justin Thank you With Regards M. Kavyashree On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear gromacs users, I wanted to know the steps to be followed in order to generate a topology for a new ligand. I went through the mailing list and http://www.gromacs.org/__Documentation/How-tos/__Parameterization http://www.gromacs.org/Documentation/How-tos/Parameterization but was not clear. All force fields are different, and since you haven't said which one you're trying to use there's nothing that anyone can tell you. Read the primary literature for the force field you want to use and follow the procedure laid out therein. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology for a new ligand
On 12/08/2011 1:48 AM, Kavyashree M wrote: Dear users, I was mentioning about OPLSAA force field for ATP and other small molecule. I just wanted to know the procedure to be followed and some guidance from people who have created topologies for such molecules manually. I am going through chapter 5 of the manual. But wanted some useful suggestions. The link you mentioned, and links from it contain all the readily-available information. For ATP, you may well find a validated topology in the published literature. Mark Thank you With Regards M. Kavyashree On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear gromacs users, I wanted to know the steps to be followed in order to generate a topology for a new ligand. I went through the mailing list and http://www.gromacs.org/Documentation/How-tos/Parameterization but was not clear. All force fields are different, and since you haven't said which one you're trying to use there's nothing that anyone can tell you. Read the primary literature for the force field you want to use and follow the procedure laid out therein. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology for nBuOH
Juliana Angeiras wrote: Hi, I'm trying to include parameters of n-butanol in the topology file (below) (i'm not using opls or other force field for butanol), but when i run the grompp program, I obtain the following message: Fatal error: Atomtype Hb not found How can I fix this problem? Your directives are out of order. If you define new atomtypes, etc. they have to be defined before they can be used. See Chapter 5 of the manual. -Justin Thanks Topology file: ; Include forcefield parameters #include oplsaa.ff/forcefield.itp ; Include forcefield parameters #include oplsaa.ff/tip5p.itp [ moleculetype ] ; name nrexcl BuOH 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 Hb 1 BuOH HO 1 0.38 1.0080 2 O 1 BuOH OH 1 -0.66 15.9994 3 C 1 BuOH CA 1 0.40 12.0110 4 C 1 BuOH CB 1 -0.22 12.0110 5 C 1 BuOH CC 1 -0.22 12.0110 6 C 1 BuOH CD 1 -0.33 12.0110 7 H 1 BuOH HA 1 -0.06 1.0080 8 H 1 BuOH HB 1 -0.06 1.0080 9 H 1 BuOH HC 1 0.11 1.0080 10 H 1 BuOH HD 1 0.11 1.0080 11 H 1 BuOH HE 1 0.11 1.0080 12 H 1 BuOH HF 1 0.11 1.0080 13 H 1 BuOH HG 1 0.11 1.0080 14 H 1 BuOH HF 1 0.11 1.0080 15 H 1 BuOH HG 1 0.11 1.0080 [ atomtypes ] ; name at.num mass charge ptype V(c6) W(c12) Hb 1 1.0080 0.38 A 0.4149611E-07 0.9737356E-04 O 815.9994-0.66 A 0.9722461E-06 0.1247853E-02 C 612.0110 0.40 A 0.4895634E-05 0.2791672E-02 C 612.0110-0.22 A 0.4895634E-05 0.2791672E-02 C 612.0110-0.33 A 0.4895634E-05 0.2791672E-02 H 1 1.0080-0.06 A 0.4415162E-06 0.5131711E-03 H 1 1.0080 0.11 A 0.4415162E-06 0.5131711E-03 [ bondtype ] ; ai aj funct c0 c1 HB O 1 0.10900 462750.4 O C 1 0.14300 376560.0 C C 1 0.15300 265265.6 H C 1 0.10800 284512.0 [ angletype ] ; aiajak func c0c1 COHB 1108.000460.240 CCO 1108.000418.400 CCC 1112.000488.273 HCH 1109.470292.000 [ dihedrals ] 1 2 3 4 30.41840 1.25520 0.0 -1.67360 0.0 0.0 2 3 4 5 32.87441 0.58158 2.09200 -5.54799 0.0 0.0 3 4 5 6 32.92880 -1.46440 0.20920 -1.67360 0.0 0.0 [ nonbond_params ] ; i j func V(c6) W(c12) H H 1 0.4149611E-07 0.9737356E-04 H HW 1 0.4149611E-07 0.9737356E-04 H C 1 0.4415162E-06 0.5131711E-03 H O 1 0.1927397E-06 0.3416812E-03 H OW 1 0.1927397E-06 0.3416812E-03 H Hb 1 0.4149611E-07 0.9737356E-04 HW HW 1 0.000E+00 0.000E+00 HW C 1 0.4415162E-06 0.5131711E-03 HW O 1 0.000E+00 0.000E+00 HW OW 1 0.000E+00 0.000E+00 HW Hb 1 0.4149611E-07 0.9737356E-04 C C 1 0.4895634E-05 0.2791672E-02 C O 1 0.2159724E-05 0.1866537E-02 C OW 1 0.2159724E-05 0.1866537E-02 C Hb 1 0.4415162E-06 0.5131711E-03 O O 1 0.9722461E-06 0.1247853E-02 O OW 1 0.1562282E-05 0.1785000E-02 O Hb 1 0.000E+00 0.000E+00 OW OW 1 0.2510400E-05 0.2552000E-02 OW Hb 1 0.000E+00 0.000E+00 Hb Hb 1 0.4149611E-07 0.9737356E-04 [ system ] ; Name BuOH in water [ molecules ] ; Compound#mols BuOH 343 SOL185 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology
chitrala kumaraswamynaidu wrote: Iam working with a NMR protein containing Zn ions. After generating topology file using pdb2gmx, it is generating topology files containing Protein and ions separately. How can i solve this. pdb2gmx -chainsep (-merge in old versions). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology files for ligands in MD Simulation under OPLS AA force field
mirc...@sjtu.edu.cn wrote: Dear All: I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom from the ligands? 2, how to define the charges of each atom? I know that, when the atom type is defined, there will be a corresponding charge to this atom type. Does it safe to use this charge in the simulations on the ligands (since these charges are designed for amino acids)? Proper parameterization is a difficult task. See, for instance: http://www.gromacs.org/Documentation/How-tos/Parameterization 3,When the atom type and the charge of atom are defined, how to prepare the file in the GROMACS format? Does there easier method to prepare such files than manually? There is at least one script (topolgen.pl) in the User Contributions section of the Gromacs site, but it is not terribly intelligent and the resulting topology should not be viewed as something that you should use without proper validation. http://www.gromacs.org/Downloads/User_contributions/Other_software Otherwise, break out Chapter 5 of the manual (something you should probably do anyway) and your favorite text editor. -Justin Thank you very much for your time and your kindness. I really appreciate if any one can share their experience in preparing the topology files for ligands used under OPLS_AA force field and GROMACS package. Sincerely Yours Ruo-Xu Gu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology with all hydrogens
Hi Mohsen, So you want to have a topology with all atoms for use in a united atom force field? Seems a bit awkward... PRODRG will only include polar hydrogens, in accordance with the GROMOS force field. It won't be a particular trustworthy topology, though, but you've probably caught the words of caution expressed regularly on this list. Cheers, Tsjerk On Feb 6, 2011 9:42 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I want to generate a topology file in 43A1 force field for a small molecule. Of course I want one which contains all hydrogens in that. PRODRG doesn't generate like this.do you know another server with these conditions? Thanks in advance Mohsen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology with all hydrogens
Dear Dr.Tsjerk I know it.I know PRODRG is not very valid for evaluating free energies(According to Dr.Justin article) too. But the problem is here: If I know all of hydrigenes are polar,how can I have a topology with all of them? Actually there are so many polar H in my small molecules which are not included in topology file!! These can change the number of Hydrogen bonds and as a resut my binding free energy!!! I want to do a new work about these,I have something excellent in my mind. I only need a topology file with all hydrogenes in 43A1 force field. Is there any way(except manually adding hydrogenes)? Please let me know. I will present a new and excellent method instead of using PRODRG Thanks in advance Mohsen On Sun, Feb 6, 2011 at 1:23 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, So you want to have a topology with all atoms for use in a united atom force field? Seems a bit awkward... PRODRG will only include polar hydrogens, in accordance with the GROMOS force field. It won't be a particular trustworthy topology, though, but you've probably caught the words of caution expressed regularly on this list. Cheers, Tsjerk On Feb 6, 2011 9:42 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I want to generate a topology file in 43A1 force field for a small molecule. Of course I want one which contains all hydrogens in that. PRODRG doesn't generate like this.do you know another server with these conditions? Thanks in advance Mohsen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology with all hydrogens
Hi Mohsen, Now I wouldn't want to get in the way of excellent ideas :) Check the PRODRG FAQ. It is explained there (somewhere) how to force inclusion of hydrogens. Cheers, Tsjerk On Feb 6, 2011 11:39 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk I know it.I know PRODRG is not very valid for evaluating free energies(According to Dr.Justin article) too. But the problem is here: If I know all of hydrigenes are polar,how can I have a topology with all of them? Actually there are so many polar H in my small molecules which are not included in topology file!! These can change the number of Hydrogen bonds and as a resut my binding free energy!!! I want to do a new work about these,I have something excellent in my mind. I only need a topology file with all hydrogenes in 43A1 force field. Is there any way(except manually adding hydrogenes)? Please let me know. I will present a new and excellent method instead of using PRODRG Thanks in advance Mohsen On Sun, Feb 6, 2011 at 1:23 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, So ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CT 12.011000 -0.18 A 0.35 0.276144 HC 1.008000 0.06 A 0.25 0.125520 ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CT 1PENT CT 1 0. 12.0110 2 CT 1PENT CT 1 -0.1800 12.0110 3 CT 1PENT CT 1 -0.1800 12.0110 4 CT 1PENT CT 1 -0.1800 12.0110 5 CT 1PENT CT 1 -0.1800 12.0110 6 HC 1PENT HC 1 0.0600 1.0080 7 HC 1PENT HC 1 0.0600 1.0080 8 HC 1PENT HC 1 0.0600 1.0080 9 HC 1PENT HC 1 0.0600 1.0080 10 HC 1PENT HC 1 0.0600 1.0080 11 HC 1PENT HC 1 0.0600 1.0080 12 HC 1PENT HC 1 0.0600 1.0080 13 HC 1PENT HC 1 0.0600 1.0080 14 HC 1PENT HC 1 0.0600 1.0080 15 HC 1PENT HC 1 0.0600 1.0080 16 HC 1PENT HC 1 0.0600 1.0080 17 HC 1PENT HC 1 0.0600 1.0080 [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) 1 2 1 0.1529 224262.4 1 3 1 0.1529 224262.4 1 4 1 0.1529 224262.4 1 5 1 0.1529 224262.4 2 6 1 0.1090 284512.0 2 7 1 0.1090 284512.0 2 8 1 0.1090 284512.0 3 9 1 0.1090 284512.0 310 1 0.1090 284512.0 311 1 0.1090 284512.0 412 1 0.1090 284512.0 413 1 0.1090 284512.0 414 1 0.1090 284512.0 515 1 0.1090 284512.0 516 1 0.1090 284512.0 517 1 0.1090 284512.0 [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) 2 1 3 1 112.70 488.2728 2 1 4 1 112.70 488.2728 2 1 5 1 112.70 488.2728 3 1 4 1 112.70 488.2728 3 1 5 1 112.70 488.2728 4 1 5 1 112.70 488.2728 1 2 6 1 110.70 313.8000 1 2 7 1 110.70 313.8000 1 2 8 1 110.70 313.8000
Re: [gmx-users] topology file for two molecules
Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
O.K Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include tertpentane.itp #include methylcage.itp ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Gavin Melaugh wrote: Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. I can't give a better explanation than what is already in the manual, specifically section 5.3.3 ([nonbond_params] and whether or not you need it). Whether or not you need [pairs] depends on the underlying mechanics of the force field you're using. See section 5.3.5. -Justin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include tertpentane.itp #include methylcage.itp ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --
Re: [gmx-users] topology file for two molecules
Justin Cheers, I had just posted a more general query prior to you getting back? It is perhaps not as vague. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. I can't give a better explanation than what is already in the manual, specifically section 5.3.3 ([nonbond_params] and whether or not you need it). Whether or not you need [pairs] depends on the underlying mechanics of the force field you're using. See section 5.3.5. -Justin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include tertpentane.itp #include methylcage.itp ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] topology for a cyclic peptide
Rebeca García Fandiño wrote: Hi, I am trying to get the topology of a cyclic peptide, but when I try to do pdb2pgx I get automatically the correction to a terminal one. I have looked in the Gromacs list and I only have found a entry about it, http://osdir.com/ml/science.biology.gromacs.user/2006-08/msg00297.html but I cannot find a solution from there. Does anyone have any idea about it, please? You'll have to do a bit of manual work yourself. I don't entirely understand the approach quoted above, but running pdb2gxm -ter (choosing None for both termini), then adding all necessary bonded information (bonds, angles, dihedrals, and impropers) manually should do the trick. -Justin Thanks a lot for your help. Best wishes, Rebeca García Santiago de Compostela University Spain http://serviciosmoviles.es.msn.com/hotmail/movistar.aspx Hotmail prepara novedades y sorpresas en breve, ¡estate atento! http://explore.live.com/windows-live-hotmail -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology files for OPLSAA and RESP charges
Hello, I just read your message... As far as I know, the RESP charge method is mainly employed forthe AMBER force field and associated (GLYCAM, GAFF, etc). I would check first that RESP is compatible with the method employed to develop OPLS-AA. Note that the AmberTools provide some scripts to calculate RESP charges. I have also used the RED server (http://q4md-forcefieldtools.org/REDS/), which is quite convenient when you want to take into account different conformations of a same molecule. In all cases, you will need to provide to those tools the molecular electrostatic potential of your molecule. None of this tools can generate a Gromacs topology file, however. Regards, Nicolas Tanos C. C. Franca a écrit : Dear GROMACS users, I'm trying to start running jobs using RESP charges and OPLSAA force field but I am facing problems to generate the RESP charges and the topology files for the OPLSAA force field. Does someone knows a software to calculate the RESP charges for the ligands and/or, also, to generate the .itp files for OPLSAA ? With the best regards, Tanos C. C. Franca. attachment: nicolas_sapay.vcf-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology files for OPLSAA and RESP charges
- Original Message - From: Tanos C. C. Franca ta...@ime.eb.br Date: Monday, May 24, 2010 1:03 Subject: [gmx-users] Topology files for OPLSAA and RESP charges To: gmx-users@gromacs.org Dear GROMACS users, I'm trying to start running jobs using RESP charges and OPLSAA force field but I am facing problems to generate the RESP charges and the topology files for the OPLSAA force field. Does someone knows a software to calculate the RESP charges for the ligands and/or, also, to generate the .itp files for OPLSAA ? The general advice is here: http://www.gromacs.org/Documentation/How-tos/Parametrization. I am not aware of an OPLSAA-specific helper tool. Be wary of presupposing that use of RESP is correct for OPLSAA. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology and force fields
Hello I think what you have been told is wrong. You need to include both ffcharmm27.itp and tip3p.itp as the atomtypes in your tip3p.itp will otherwise not be defined. There is an easy way to check though - take out the include ffcharmm27.itp and try to run grompp on your new topology. My bet would be that it won't work and, if you are using rigid molecules, it will tell you that it finds a settles section in the wrong place. ciao Gareth On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi lumngwe...@gmail.com wrote: Hello all, Below are the contents of a water1.top file that I used to simulate 2000 molecules of TIP3P water (NPT). I made this topology file according to the pattern on page 114 of the manual (topology for Urea in water). My diffusion coefficient, viscosity and radial distribution functions matched those for tip3p water in literature. Recently I was told that I did not need to use another force field in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield on its own. Could this be true? I just wanted to verify the authenticity of my simulation. If the structure of the topology below is not correct, please let me know. ; The force field files to be included #include ffcharmm27.itp ; Include TIP3P water topology #include tip3p.itp [ system ] Pure Water [ molecules ] ;molecule name number SOL 1936 SOL64 I appreciate your answers. Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology and force fields
Gareth Tribello wrote: Hello I think what you have been told is wrong. You need to include both ffcharmm27.itp and tip3p.itp as the atomtypes in your tip3p.itp will That is exactly what was in the original topology, no problem there. There are no [atomtypes] in tip3p.itp; these are defined by ff*nb.itp. otherwise not be defined. There is an easy way to check though - take out the include ffcharmm27.itp and try to run grompp on your new topology. My bet would be that it won't work and, if you are using rigid molecules, it will tell you that it finds a settles section in the wrong place. More likely grompp will raise a fatal error that the atomtypes are not found, before anything else happens :) You could, in theory, run a simulation of just water by specifying a all the directives listed at the parameter level (Table 5.3 and section 5.7.1 in the manual) in the .top file, then #include tip3p.itp - that's all that's really necessary. Using the #include mechanism with an existing force field solves this problem for you. The combination rules of the Gromos, OPLS, and CHARMM force fields are all different (manual section 5.3.3, equations 5.3 and 5.4), but I don't know offhand what effect that might have on your results. TIP3P itself is not really a force field, it is a set of parameters that model a single molecule. The interaction function (the other part of a force field) is defined by the functional forms defined by ff*.itp in the parameter-level directives. Otherwise, the atom types and nonbonded parameters for a water model should be uniform, that is, independent of the force field chosen (with the only modifications being conversion between sigma/epsilon and C6/C12, per force field requirements). Your treatment of other .mdp parameters will affect your results, as well, but many of these should be prescribed in the derivation of the parameters or in subsequent modifications and extensions. -Justin ciao Gareth On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi lumngwe...@gmail.com mailto:lumngwe...@gmail.com wrote: Hello all, Below are the contents of a water1.top file that I used to simulate 2000 molecules of TIP3P water (NPT). I made this topology file according to the pattern on page 114 of the manual (topology for Urea in water). My diffusion coefficient, viscosity and radial distribution functions matched those for tip3p water in literature. Recently I was told that I did not need to use another force field in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield on its own. Could this be true? I just wanted to verify the authenticity of my simulation. If the structure of the topology below is not correct, please let me know. ; The force field files to be included #include ffcharmm27.itp ; Include TIP3P water topology #include tip3p.itp [ system ] Pure Water [ molecules ] ;molecule name number SOL 1936 SOL64 I appreciate your answers. Lum -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology
tekle...@ualberta.ca wrote: Dear Justin, First of all thank you for your help.. I have developed the toplogy file for my molecule using the PRODRG server. But the topology did not include properly the carboxylic acid functional group ( with proton) instead the software assumes both oxygens as identical due to resonance. Therefore I want to modify my topology .what do I need to do. From the PRODRG FAQ: Q: PRODRG doesn't properly protonate my molecule. A: This can be fixed by adding the command ADDHYD atomname or DELHYD atomname to your input drawing/PDB file. No need to hack the topology. Run PRODRG once to identify which atom name it will assign to the oxygens, then follow the instructions above. -Justin In side my topology (initial) === 44 CH1 1 UNK CA130.14313.0190 45 C 1 UNK C 130.37212.0110 46 OM 1 UNK OXT 13-0.757 15.9994 47 OM 1 UNK O 13-0.758 15.9994 MODIFIED to the following topology 44 CH1 1 UNK CA13 XXX 13.0190 45 C 1 UNK C 13 XXX 12.0110 46 O 1 UNK OXT 13 XXX 15.9994 47 OA 1 UNK O 13 XXX 15.9994 48 HO 1 UNK HAA 13 XXX 1.00800 === XXX refers to a charge of each .. How can I allocate a charge distribution for each united atom molecule in the modified topology ... Remark I checked the .RTP file and I have found the following information for the [ ASPH] residue CG C 0.53000 2 OD1 O-0.38000 2 OD2OA-0.54800 2 HD2HO 0.39800 2 But in this case eventhough this describes for the carboxilic acid functional group . It does not include CH1 in the same group.. what do I need to do to Example CA CH1 XXX 2 CG C 0.53000 2 OD1 O-0.38000 2 OD2OA-0.54800 2 HD2HO 0.39800 2 XX is the new charge for CH1 which I do not know. can you help. or simply I have to put 0.0 have a great day Rob *** The entire Topology is the following ; nr type resnr resid atom cgnr charge mass 1 CH3 1 UNK CAZ 10.000 15.0350 2 CH2 1 UNK CAK 10.000 14.0270 3 CH2 1 UNK CBS 20.000 14.0270 4 CH2 1 UNK CBL 20.000 14.0270 5 CH2 1 UNK CBG 30.000 14.0270 6 CH2 1 UNK CBM 30.000 14.0270 7 CH1 1 UNK CBA 30.000 13.0190 8 CH2 1 UNK CBD 30.000 14.0270 9 CH2 1 UNK CBE 30.000 14.0270 10 CH2 1 UNK CBF 40.000 14.0270 11 CH2 1 UNK CBJ 40.000 14.0270 12 CH2 1 UNK CBN 50.101 14.0270 13 CH3 1 UNK CBT 50.057 15.0350 14 NR6* 1 UNK NBU 50.069 14.0067 15CB 1 UNK CBP 50.346 12.0110 16 O 1 UNK OCB 5 -0.573 15.9994 17CB 1 UNK CAG 60.351 12.0110 18 O 1 UNK OCA 6 -0.565 15.9994 19 CH1 1 UNK CBI 60.178 13.0190 20 CR61 1 UNK CBO 60.018 13.0190 21 CR61 1 UNK CAV 60.018 13.0190 22CB 1 UNK CAN 70.000 12.0110 23CB 1 UNK CAR 70.000 12.0110 24CB 1 UNK CAX 80.000 12.0110 25CB 1 UNK CBC 80.000 12.0110 26 CR61 1 UNK CBH 80.000 13.0190 27 CR61 1 UNK CAW 80.000 13.0190 28 CH1 1 UNK CAQ 90.074 13.0190 29CB 1 UNK CAM 90.001 12.0110 30 CR61 1 UNK CAU 9 -0.037 13.0190 31 CR61 1 UNK CAI 9 -0.038 13.0190 32CB 1 UNK CAC100.003 12.0110 33CB 1 UNK CAE100.442 12.0110 34 O 1 UNK OBX10 -0.448 15.9994 35CB 1 UNK CAB100.003 12.0110 36CB 1 UNK CAF110.004 12.0110 37CB 1 UNK CAJ110.004 12.0110 38 CR61 1 UNK CAP11 -0.008 13.0190 39 CR61 1 UNK CAH12 -0.013 13.0190 40CB 1 UNK CAA120.003 12.0110 41CB 1 UNK CAD120.411 12.0110 42 O 1 UNK OBW12 -0.483 15.9994 43 NR6* 1 UNK N120.082 14.0067 44 CH1
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
Antoine Delmotte wrote: Thank you very much for your quick response, Justin. I guess I need a little bit more practise to make the parametrization myself. Do you have any clues on where I could find published parameters? Are there databases for this or something similar? Literature searching is your best bet. But as far as I know, there is no database of previously-published parameters. Understanding the intrinsics of the force field (the original derivation and subsequent improvements) will be the most useful for you to understand the intrinsics of the force field. If you're dead set on using OPLS, then you probably have (a lot) of work cut out for you. Parameters for phosphorylated Ser, Thr, and Tyr for Gromos96 43a1 were published some time ago. -Justin Regards, Antoine Le 5/02/2010 18:23, Justin A. Lemkul a écrit : Antoine Delmotte wrote: Dear gmx-users, I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Search the literature to see if anyone has published parameters for it. Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? That's what Chapter 5 of the manual is for, provided you have reliable parameters (see below). Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. If MD is completely new to you, and you are unable to find previously published and validated parameters, the parameterization of a new species is likely not a suitable task. Parameterization is an expert topic, and it can take many months or years to develop reliable parameters, even if you know what you are doing at the very start. Be forewarned: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin I thank you in advance. Best regards, Antoine Hotmail : une messagerie fiable avec la protection anti-spam performante de Microsoft Inscrivez-vous https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
Thank you very much for your quick response, Justin. I guess I need a little bit more practise to make the parametrization myself. Do you have any clues on where I could find published parameters? Are there databases for this or something similar? Regards, Antoine Le 5/02/2010 18:23, Justin A. Lemkul a écrit : Antoine Delmotte wrote: Dear gmx-users, I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Search the literature to see if anyone has published parameters for it. Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? That's what Chapter 5 of the manual is for, provided you have reliable parameters (see below). Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. If MD is completely new to you, and you are unable to find previously published and validated parameters, the parameterization of a new species is likely not a suitable task. Parameterization is an expert topic, and it can take many months or years to develop reliable parameters, even if you know what you are doing at the very start. Be forewarned: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin I thank you in advance. Best regards, Antoine Hotmail : une messagerie fiable avec la protection anti-spam performante de Microsoft Inscrivez-vous https://signup.live.com/signup.aspx?id=60969 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
Thank you very much for this, Bruce. It will help me, for sure. Could you just let me know where you found the parameters or how you generated them? Thanks in advance. Regards, Antoine Le 5/02/2010 22:39, Bruce D. Ray a écrit : On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte antoinedelmo...@hotmail.com wrote: I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. The charges probably need a little more work, but this might be a start towards an rtp file for phosphothreonine to add to ffoplsaa.rtp. [ TPO ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_1580.205 2 HBopls_1400.060 2 OG1opls_447 -0.700 2 Popls_4451.795 3 O1Popls_446 -1.120 3 O2Popls_446 -1.120 3 O3Popls_446 -1.120 3 CG2opls_135 -0.180 4 HG21opls_1400.060 4 HG22opls_1400.060 4 HG23opls_1400.060 4 Copls_2350.500 5 Oopls_236 -0.500 5 [ bonds ] N H NCA CAHA CACB CA C CBHB CB OG1 CB CG2 OG1 P O1P P O2P P O3P P CG2 HG21 CG2 HG22 CG2 HG23 C O -C N [ dihedrals ] ; override some of the typebased dihedrals NCACB OG1dih_SER_THR_chi1_N_C_C_O CCACB OG1dih_SER_THR_chi1_CO_C_C_O CACB OG1 HG1dih_SER_THR_chi2_C_C_OH_HO [ impropers ] -CCA N Himproper_Z_N_X_Y CA+N C Oimproper_O_C_X_Y I hope that helps. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
Thank you very much Fairuz. I will try this. Le 6/02/2010 1:20, fairuz zulkifli a écrit : to create itp file with OPLS force feild, you can try use GAMESS. -fairuz- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
On Sat, February 6, 2010 at 11:08:30 AM, Antoine Delmotte antoinedelmo...@hotmail.com wrote: Thank you very much for this, Bruce. It will help me, for sure. Could you just let me know where you found the parameters or how you generated them? Most of the parameters came from the entry for threonine in ffoplsaa.rtp The remainder came from running the most recent beta test version of topolbuild 1.3 with the command line /usr/local/bin/topolbuild -dir /usr/local/topolbuild -ff oplsaa -n tpo_pep -charge which generates an OPLSaa topology with parameters found originally in the Gromacs OPLSaa installation against a short peptide containing phosphothreonine and sets the atom charges to the OPLSaa atom type charges. I then edited the threonine entry from ffoplsaa.rtp according to add in the phosphate atom types, and change those atom types that are altered by the presence of the phosphate. Finally, I adjusted the charge on the phosphorous from the charge given in ffoplsaanb.itp in order to have the total charge come out as -2 for a fully ionized phosphate. The exact ionization would depend on pH, of course, and I would have to run the command for protonated TPO (TPH ? or TPH2 ? for the mono- and di-protonated species?) to further correct atom types and charges. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
Antoine Delmotte wrote: Dear gmx-users, I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Search the literature to see if anyone has published parameters for it. Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? That's what Chapter 5 of the manual is for, provided you have reliable parameters (see below). Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. If MD is completely new to you, and you are unable to find previously published and validated parameters, the parameterization of a new species is likely not a suitable task. Parameterization is an expert topic, and it can take many months or years to develop reliable parameters, even if you know what you are doing at the very start. Be forewarned: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin I thank you in advance. Best regards, Antoine Hotmail : une messagerie fiable avec la protection anti-spam performante de Microsoft Inscrivez-vous https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte antoinedelmo...@hotmail.com wrote: I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. The charges probably need a little more work, but this might be a start towards an rtp file for phosphothreonine to add to ffoplsaa.rtp. [ TPO ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_1580.205 2 HBopls_1400.060 2 OG1opls_447 -0.700 2 Popls_4451.795 3 O1Popls_446 -1.120 3 O2Popls_446 -1.120 3 O3Popls_446 -1.120 3 CG2opls_135 -0.180 4 HG21opls_1400.060 4 HG22opls_1400.060 4 HG23opls_1400.060 4 Copls_2350.500 5 Oopls_236 -0.500 5 [ bonds ] N H NCA CAHA CACB CA C CBHB CB OG1 CB CG2 OG1 P O1P P O2P P O3P P CG2 HG21 CG2 HG22 CG2 HG23 C O -C N [ dihedrals ] ; override some of the typebased dihedrals NCACB OG1dih_SER_THR_chi1_N_C_C_O CCACB OG1dih_SER_THR_chi1_CO_C_C_O CACB OG1 HG1dih_SER_THR_chi2_C_C_OH_HO [ impropers ] -CCA N Himproper_Z_N_X_Y CA+N C Oimproper_O_C_X_Y I hope that helps. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology and rtp file
irene farabella wrote: Hello Gmx Usrs, I am new to Gromacs. I am trying to simulate a protein-membrane complex using berger-oplsaa combination . I have created a topology Have you properly modified the Berger parameters for use with OPLS-AA? Otherwise, the results you will get will be nonsense :) file for the protein using pdb2gmx in order to then build up the topology for my system using the include file mechanism. After that I tried to use my system.top in grompp ( grompp -f xx.mdp -c system.pdb -p system.top -o out.tpr ) but I get a warning about atoms in top and pdb does not match. I went trough the mailing list Is system.pdb the cleaned up output from pdb2gmx? It is also better to post the actual error message. The topology and coordinate file may not match in terms of atom names or in terms of the number of coordinates, which are both very different problems. I guess you are referring to a naming mismatch? but I have still doubt. I checked where were the differences. It seems that the order of the aromatic ring in the pdb and in the top didn't match. To be clear (tyr as example but the same problem occur with his): .pdb .top N N HNH If this is what's in your .pdb file, then you aren't using the pdb2gmx output, are you? CA CA HA HA CB CB HB1 HB1 HB2 HB2 CG CG CD1 CD1 HD1 HD1 CE1 CD2 HE1 HD2 CZ CE1 OH HE1 HH CE2 CD2 HE2 HD2 CZ CE2 OH HE2 HH CC O O Is this because the .top seems follow the order presents in the rtp file that I have (am I right?). Yes, pdb2gmx will output according to the .rtp entry. Assuming that this is the case I am wondering if changing the atoms order in the rtp from: [ TYR ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 3 CD1opls_145 -0.115 4 HD1opls_1460.115 4 CD2opls_145 -0.115 5 HD2opls_1460.115 5 CE1opls_145 -0.115 6 HE1opls_1460.115 6 CE2opls_145 -0.115 7 HE2opls_1460.115 7 CZopls_1660.150 8 OHopls_167 -0.585 8 HHopls_1680.435 8 Copls_2350.500 9 Oopls_236 -0.500 9 to: [ TYR ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 3 CD1opls_145 -0.115 4 HD1opls_1460.115 4 CE1opls_145 -0.115 6 HE1opls_1460.115 6 CZopls_1660.150 8 OHopls_167 -0.585 8 HHopls_1680.435 8 CE2opls_145 -0.115 7 HE2opls_1460.115 7 CD2opls_145 -0.115 5 HD2opls_1460.115 5 Copls_2350.500 9 Oopls_236 -0.500 9 can that have a further effect since it seems that the file handling is based on line position and not atoms name. If you re-arrange the .rtp file, you'll have to start all over again, since only pdb2gmx uses the .rtp files. I doubt this is meaningful. If you've got a .pdb file with HN as the amide proton, then it won't match the topology, which specifies this atom as H. There will still be a name mismatch, but not an order mismatch, which simply indicates to me that you are using the wrong coordinate file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology file in .dat format
Hi Subarna, There is no .dat format for topologies. It may be named .dat, but the inside (format) is what matters. If you're confident it is gromos96 format, you can #include it the same way as other molecule definition topology files. Do mind that there's quite a difference between GROMOS96 43a1, 43a2, 45a3, 53a5 and 53a6... Cheers, Tsjerk On Tue, Nov 10, 2009 at 8:30 AM, subarna thakur thakur.suba...@yahoo.co.in wrote: Hello I have a gromos96 topology file for a ligand and it is in xx.dat format.How do I include this file in my gromacs version 4.0 simulation of a protein? Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology file
abhijit kayal wrote: Hi, Myself Abhijit Kayal,student at IITD.Is it possible to create a topology file by Amber or some other molecular dynamics software for nonstandard molecules such as n-butane and can these topology files be used in gromacs?please reply. Yes. There are scripts in the User Contributions section of the website that will do exactly that. -Justin Abhijit Kayal IIT Delhi ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology info for specific bond between atoms in different molecules
ucsd mail wrote: Hi There, I am a new user of Gromacs and want to work on carbon nanotubes. I want to simulation carbon nanotube(cnt) bonded with polymers in water. And it will be much better to consider cnt and the bonded polymer as separate molecules, instead of one molecule. I can create the .itp file for both the nanotube and the polymer chain, and include them in the .top file. But I do not know how to describe the bond betwen the cnt and the polymer. You cannot have a bonded interaction between atoms that belong to different [ moleculetype ] directives. So you will need to make a hybrid of the nanotube and the polymer. Depending on what sense you think it will be better to have them as separate molecules, you may wish to define index groups with make_ndx for whatever use you have in mind. Mark Currently my .top file looks like this: (Thanks a lot!) *** [ defaults ] ; nbfunccomb-rulegen-pairs fudgeLJ fudgeQQ 11 [ atomtypes ] ; type mass charge ptype c6 c12 C 12.0 0.0 A0.00.0 X1.0e10 0.0 A0.00.0 OW15.994-0.82 A0.00.0 H 1.008 0.41 A0.00.0 ...more info [ nonbond_params ] ; aiaj funct aij bij C C 12.8768001E-34.691598E-6 OWOW 12.6169064E-32.633236E-6 COW 11.3176287E-31.388472E-6 ...more info [ bondtypes ] ; i j func b0 kb beta C C 3 0.1418 478.9 21.867 ...more info [ angletypes ] ;i j k func th0 cth C C C 2 120.0 562.2 ...more info [ dihedraltypes ] ; i jfunc phi0 cp mult C C 1 180.012.562 ...more info #include cnt_test.itp #include FLEXSPC.itp #include polymer.itp [ system ] CNT_H2O [ molecules ] CNT 1 SOL 1419 POL 2 * I read the manual and found an example that include bonds in topology file like below. The atom IDs are specified instead of atom type. Can I do this for atom (ID) in different molecules? Thanks. * [ bonds ] ; ai aj funct b0 kb 3 4 1 1.00e-01 3.744680e+05 3 5 1 1.00e-01 3.744680e+05 6 7 1 1.00e-01 3.744680e+05 6 8 1 1.00e-01 3.744680e+05 1 2 1 1.23e-01 5.020800e+05 1 3 1 1.33e-01 3.765600e+05 1 6 1 1.33e-01 3.765600e+05 * Regards, Stone ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology and residue database?
Joseph Johnson wrote: Is there still a topology and peptide residue on the Gromacs website? It's mentioned in the documentation but I can't seem to find it. The user contributions? You can still access all of the old site's content by appending old to the URL (i.e., http://oldwww.gromacs.org), and the user-contributed topologies and stuff are at: http://oldwww.gromacs.org/component/option,com_docman/task,cat_view/gid,39/Itemid,26/ -Justin Thanks :) Hotmail® has ever-growing storage! Don’t worry about storage limits. Check it out. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of HEO compound in .rtp for G96 ff
Egidijus Kuprusevicius wrote: Hello, could anyone help me and check if the topology of the HEO compound was done properly for G96 ff? Thanks in advance. I couldn't find it in the database, so I decided to try to make it manualy. Any comments would be appreciated. Or maybe does exists any programs who does the work? It would help to know what HEO is, and which version of Gromos96 you are attempting to use. If this is some sort of HEME derivative, as it appears, you can probably verify much of the topology, since HEME exists in the .rtp file for all the Gromos96 variants. It is not possible to simply look at a topology and verify if it is correct. Parameterization requires you to verify some sort of experimental observable to justify the parameters you have assigned. -Justin [ HEO ] [ atoms ] FEFE 0.4 0 NANR-0.1 0 NBNR-0.1 0 NCNR-0.1 0 NDNR-0.1 0 CHA CH1 0.0 1 C1A C 0.0 2 C2A C 0.0 2 C3A C 0.0 2 C4A C 0.0 2 CMA CH3 0.0 3 CAA CH2 0.0 4 CBA CH2 0.0 4 CGA C 0.27000 5 O1AOM-0.63500 5 O2AOM-0.63500 5 CHB CH1 0.0 6 C1B C 0.0 7 C2B C 0.0 7 C3B C 0.0 7 C4B C 0.0 7 CMB CH3 0.0 8 C11 C 0.38000 9 O11 O-0.38000 9 CHC CH1 0.010 C1C C 0.011 C2C C 0.011 C3C C 0.011 C4C C 0.011 CMC CH3 0.012 CAC CR1 0.013 CBC CH2 0.013 CHD CH1 0.014 C1D C 0.015 C2D C 0.015 C3D C 0.015 C4D C 0.015 CMD CH3 0.016 CAD CH2 0.017 CBD CH2 0.017 CGD C 0.2700018 O1DOM-0.6350018 O2DOM-0.6350018 C12 CH2 0.019 C13 CH2 0.019 C14 CH2 0.020 C15 CH1 0.020 C16 CH3 0.020 C17 CH2 0.020 C18 CH2 0.021 C19 CH2 0.022 C20 CH1 0.022 C21 CH3 0.022 C22 CH2 0.022 C23 CH2 0.023 C24 CH2 0.024 C25 CH1 0.024 C26 CH3 0.024 C27 CH3 0.024 [ bonds ] FENAgb_34 FENBgb_34 FENCgb_34 FENDgb_34 NA C1Agb_13 NA C4Agb_13 NB C1Bgb_13 NB C4Bgb_13 NC C1Cgb_13 NC C4Cgb_13 ND C1Dgb_13 ND C4Dgb_13 CHA C1Agb_16 CHA C4Dgb_16 C1A C2Agb_16 C2A C3Agb_16 C2A CAAgb_26 C3A C4Agb_16 C3A CMAgb_26 C4A CHBgb_16 CAA CBAgb_26 CBA CGAgb_26 CGA O1Agb_5 CGA O2Agb_5 CHB C1Bgb_16 C1B C2Bgb_16 C2B C3Bgb_16 C2B CMBgb_26 C3B C4Bgb_16 C4B CHCgb_16 CHC C1Cgb_16 C1C C2Cgb_16 C2C C3Cgb_16 C2C CMCgb_26 C3C C4Cgb_16 C3C CACgb_26 C4C CHDgb_16 CAC CBCgb_11 CHD C1Dgb_16 C1D C2Dgb_16 C2D C3Dgb_16 C2D CMDgb_26 C3D C4Dgb_16 C3D CADgb_26 CAD CBDgb_26 CBD CGDgb_26 CGD O1Dgb_5 CGD O2Dgb_5 C3B C11gb_26 C11 O11gb_4 C11 C12gb_26 ; C, CHn - C, CHn800 C12 C13gb_26 ; C, CHn - C, CHn800 C13 C14gb_26 ; C, CHn - C, CHn800 C14 C15gb_26 ; C, CHn - C, CHn800 C15 C16gb_26 ; C, CHn - C, CHn800 C15 C17gb_26 ; C, CHn - C, CHn800 C17 C18gb_26 ; C, CHn - C, CHn800 C18 C19gb_26 ; C, CHn - C, CHn800 C19 C20gb_26 ; C, CHn - C, CHn800 C20 C21gb_26 ; C, CHn - C, CHn800 C20 C22gb_26 ; C, CHn - C, CHn800 C22 C23gb_26 ; C, CHn - C, CHn800 C23 C24gb_26 ; C, CHn - C, CHn800 C24 C25gb_26 ; C, CHn - C, CHn800 C25 C26gb_26 ; C, CHn - C, CHn800 C25 C27gb_26 ; C, CHn - C, CHn800 [ exclusions ] ; aiaj FE CHA FE C2A FE C3A FE CHB FE C2B FE C3B FE CHC FE C2C FE C3C FE CHD FE C2D FE C3D NA CMA NA CAA NA C1B NA C4B NA C1C NA C4C NA C1D NA C4D NB C1A NB C4A NB CMB NB C11 NB C1C NB C4C NB C1D NB C4D NC C1A NC
Re: [gmx-users] topology file with grompp program
วันเวลา อมรนพ wrote: Dear gmx users I want to simulate propane molecule and I use PRODGE website to generate both .gro and .top file. Then I run the grompp program and there is an error said that Fatal error: Invalid order for directive moleculetype, file topol.top, line 17 and below is my topology file of a propane molecule You must #include the appropriate force field file before you can define your molecule type. A few notes and suggestions: 1. If using the original PRODRG server, consider using the newer PRODRG 2.5 server. The original PRODRG gives ffgmx-compatible topologies. This force field is deprecated. PRODRG 2.5 is compatible with the newer Gromos96 variants. 2. Check the charges and charge groups carefully, and consider changing them. Does it make sense to have permanent dipoles in a propane molecule? -Justin ; ; ; This file was generated by PRODRG version 071121.0636 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk mailto:d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] ; name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.007 15.0350 2 CH2 1 DRG CAB 10.015 14.0270 3 CH3 1 DRG CAC 1 -0.008 15.0350 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.153334720.00.153334720.0 ; CAA CAB 2 3 10.153334720.00.153334720.0 ; CAB CAC [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1111.0 460.2111.0 460.2 ; CAA CAB CAC [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... Please help me figure out what is the error Thanks for advance Suwit ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology for oxygen molecule
Sunil Thapa wrote: Respectable Justin/Mark For the study of diffusion of oxygen in water, I tried to search the itp file for oxygen molecule but could not find. Therefore, I have tried to make it myself. Please tell me whether it is fine. [ moleculetype ] ; molname nrexcl OMOL 1 ; as there are two atoms in an oxygen molecule [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OB 1 OMOL OB1 0 0 2 OB 1 OMOL OB2 0 0 What about mass? [ bonds ] ;ai aj funct c0 c1 1 2 1 1.24400e-01 3.472866e+05; taken from Gaussian calculation. You could also get this information from spectroscopic data, I believe. That might make for an even more realistic model. [ pairtypes ] ; for non bonded interaction within each molecule with exclusion ; i j func c6 c12 OB OB 1 0.008261659 1.7392E-05;parameters from CRC Hand book of physics and chemistry. You don't need this. You are excluding nonbonded interactions between the two OB atoms (nrexcl = 1), so there shouldn't be a pairwise interaction between them. ;[ pairs ] no need of 1-4 interaction pairs as there are only two atoms. ; ai aj funct c6 c12 ; 1 2 1 0.008261659 1.7392E-05;from CRC0 [ nonbond_params ] ; OB OW 1 0.004679059 6.853E-06; using L-B rule ; OB H 1 0 0; taken from OW-H [ exclusions ] 1 2 ; because the nrexc1 is 1. Unnecessary. Again, you set nrexcl = 1, so this is taken care of. Have you defined the appropriate [atomtype] somewhere, like the ff*nb.itp that you're using? -Justin Please tell me where I am wrong. for nonbonded interaction ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology
naimah haron naimah wrote: Dear all... How to draw the structure for ionic liquid and get their PDB file? For example, we can draw the struture by using PRODRG generation server and get their PDB file. So, any suggestion to draw the structure and get their PDB file without using PRODRG generation server? Build a small one by hand in a text editor (making sure the density is suitable and there won't be steric clashes across periodic boundaries), replicate it with genbox, and equilibrate. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology file for methane.
xianghong qi wrote: Hello, Could anyone give me some suggestions about how to write a toplogy file for methane with OPLS-AA force field? Thanks in advance. For a very simple molecule like methane, it should be very straightforward to do from reading Chapter 5. -Justin -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology file for methane.
Hi, Justin: I am reading chapter 5 now. Still feel confused. I wrote methane.top file like this: ; Methane topology file ; ; The force field files to be included #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl METH 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_138 1METH C 1 -0.24 12.011 ; qtot 0.61 2 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 3 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 4 opls_140 1METH H 1 0.06 1.008 ; qtot 0.73 5 opls_140 1METH H 1 0.06 1.008 ; qtot 0.79 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp [ system ] ; Name Methane [ molecules ] ; Compound#mols METH 1 ; ;;; Then I should go to ffoplsaa.rtp file to add a new molecule like : [METH] [ atoms ] Copls_135 -0.240 1 HC1opls_1400.060 1 HC2opls_1400.060 1 HC3opls_1400.060 1 HC4opls_1400.60 1 [ bonds ] C HC1 C HC2 C HC3 C HC4 ;;; Is that reasonable? Thanks for your help. On Mon, Oct 27, 2008 at 1:54 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: xianghong qi wrote: Hello, Could anyone give me some suggestions about how to write a toplogy file for methane with OPLS-AA force field? Thanks in advance. For a very simple molecule like methane, it should be very straightforward to do from reading Chapter 5. -Justin -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology file for methane.
xianghong qi wrote: Hi, Justin: I am reading chapter 5 now. Still feel confused. I wrote methane.top file like this: ; Methane topology file ; ; The force field files to be included #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl METH 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_138 1METH C 1 -0.24 12.011 ; qtot 0.61 2 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 3 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 4 opls_140 1METH H 1 0.06 1.008 ; qtot 0.73 5 opls_140 1METH H 1 0.06 1.008 ; qtot 0.79 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp [ system ] ; Name Methane [ molecules ] ; Compound#mols METH 1 ; ;;; Then I should go to ffoplsaa.rtp file to add a new molecule like : [METH] [ atoms ] Copls_135 -0.240 1 HC1opls_1400.060 1 HC2opls_1400.060 1 HC3opls_1400.060 1 HC4opls_1400.60 1 [ bonds ] C HC1 C HC2 C HC3 C HC4 ;;; Is that reasonable? Thanks for your help. Seems fine to me. -Justin On Mon, Oct 27, 2008 at 1:54 PM, Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: xianghong qi wrote: Hello, Could anyone give me some suggestions about how to write a toplogy file for methane with OPLS-AA force field? Thanks in advance. For a very simple molecule like methane, it should be very straightforward to do from reading Chapter 5. -Justin -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Some people make the world more special just by being in it. -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of cyclohexane
I once built one from the standart opls-atoms. It is ENTIRELY UNTESTED! I have absolutely no clue how good it is. In particular the partial charges on the H and C may have to be improved. best, Jochen Here is also a pdb: TITLE One Cyclohexane REMARKTHIS IS A SIMULATION BOX CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 CA CYC 1 26.075 25.752 1.621 1.00 0.00 ATOM 2 HA1 CYC 1 26.881 25.711 0.887 1.00 0.00 ATOM 3 HA2 CYC 1 25.289 25.092 1.251 1.00 0.00 ATOM 4 CB CYC 1 25.534 27.188 1.727 1.00 0.00 ATOM 5 HB1 CYC 1 25.141 27.510 0.762 1.00 0.00 ATOM 6 HB2 CYC 1 26.351 27.869 1.969 1.00 0.00 ATOM 7 CC CYC 1 24.440 27.294 2.801 1.00 0.00 ATOM 8 HC1 CYC 1 23.568 26.715 2.493 1.00 0.00 ATOM 9 HC2 CYC 1 24.106 28.329 2.891 1.00 0.00 ATOM 10 CD CYC 1 24.941 26.784 4.162 1.00 0.00 ATOM 11 HD1 CYC 1 24.135 26.825 4.896 1.00 0.00 ATOM 12 HD2 CYC 1 25.727 27.444 4.533 1.00 0.00 ATOM 13 CE CYC 1 25.482 25.349 4.056 1.00 0.00 ATOM 14 HE1 CYC 1 24.665 24.668 3.814 1.00 0.00 ATOM 15 HE2 CYC 1 25.875 25.027 5.021 1.00 0.00 ATOM 16 CF CYC 1 26.577 25.242 2.982 1.00 0.00 ATOM 17 HF1 CYC 1 27.448 25.821 3.290 1.00 0.00 ATOM 18 HF2 CYC 1 26.911 24.208 2.892 1.00 0.00 TER ENDMDL Here is the hdb entry. Add it to ffoplsaa.hdb: CYC 6 24 HA CA CB CF 24 HB CB CA CC 24 HC CC CB CD 24 HD CD CC CE 24 HE CE CD CF 24 HF CF CE CA Here is the rtp entry. Add it to ffoplsaa.rtp and run pdb2gmx. ; cyclohexane [ CYC ] [ atoms ] CA opls_136 -0.120 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 CB opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CC opls_136 -0.120 3 HC1 opls_140 0.060 3 HC2 opls_140 0.060 3 CD opls_136 -0.120 4 HD1 opls_140 0.060 4 HD2 opls_140 0.060 4 CE opls_136 -0.120 5 HE1 opls_140 0.060 5 HE2 opls_140 0.060 5 CF opls_136 -0.120 6 HF1 opls_140 0.060 6 HF2 opls_140 0.060 6 [ bonds ] CA HA1 CA HA2 CA CF CA CB CB HB1 CB HB2 CB CC CC HC1 CC HC2 CC CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE CF CF HF1 CF HF2 Vitaly Chaban wrote: Guys, Does anybody have an already prepared topology of cyclohexane? Thanks. -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology using prodrg
Are you sure you used prodrg beta? http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta 2008/7/4, h a [EMAIL PROTECTED]: Dear users, I am modeling polymer surface. I need topology for polystyrene. I used prodrg earlier version and beta version but in both cases I get topology for only GROMOS87 force field. Can not I get topology for force filed GROMOS96 ? also can anybody let me know what is .itp file for GOMOS87 force filed ( I mean similar to GROMOS96 - ffG43a1.itp ) thank you, Sincerely --- A.Harshith(Y6001) department of Bio Science and Bioengineering, IIT Kanpur, India. http://home.iitk.ac.in/~harshith http://home.iitk.ac.in/%7Eharshith ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology for c-alpha protein model
After pdb2gmx of the whole structure, make an index file and them run another pdb2gmx choosing the c-alpha group. I hope it helps. 2008/6/20, Lillian Chong [EMAIL PROTECTED]: Dear Gromacs Users, I would like to generate a topology for a protein in which each residue is represented only by its C-alpha atom (a Go-type model). What would be the most straightforward way of creating this topology file? Thanks in advance, Lillian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology treatment in free energy calculations -possible bug
Berk Thanks for the clarification. I was aware of A-values copied to B-values, when no B-values in the FF exist, but actually this was new to me. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Berk Hess wrote: This behavior is itentional. But it can indeed be confusing. Therefore in Gromacs 4.0 a warning will be generated (and I have added a table in the manual that explains all the possible combinations). If you explicitly define parameters for the A-state, I don't see why you would want the B-parameters to be looked up based on atom-type. You would only want that when the A-state parameters are also determined by the atom type. Berk. From: Maik Goette [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: GMX-mailinglist gmx-users@gromacs.org Subject: [gmx-users] topology treatment in free energy calculations -possible bug Date: Fri, 04 Jan 2008 15:15:57 +0100 Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology treatment in free energy calculations - possible bug
On Fri, 4 Jan 2008, Maik Goette wrote: Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? it cannot be called as a bug... when you mention parameters for A state in topology explicitly then grompp will expect you to mention the B state parameters also, and if it doesn't find it, it will assign A state parameter to B state. that is quite well documented, i think, in manual. So there is no reason to think it as a bug. bharat Regards -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology treatment in free energy calculations - possible bug_2nd
Maik, It just came to my mind, that the behaviour, I described in the first mail will be quite dangerous, whenever #define statements are in the topology, cause this would lead to the insertion of the FF-values in the topology, when preprocessing, and then be copied into the B-state afterwards, even if the values are crap for the B-state... As far as treatment of A and B state parameters, I am not sure there is any solution that doesn't result in dangerous behavior in some situations. Therefore my recommendation is that anytime one is handling atoms which are being perturbed (i.e., where the B state *might* be different from the A state) both A and B state parameters be specified explicitly in the topology by the user. David Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology treatment in free energy calculations - possible bug
Maik I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 I *think* this behavior is described in the documentation. Basically, anytime A state parameters are specified in the topology and B state are omitted, A state are copied to B state. To make B state different, you have to either (a) specify them explicitly, or (b) have them looked up in the force field where they are different. So this is expected behavior. David Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] topology treatment in free energy calculations -possible bug
This behavior is itentional. But it can indeed be confusing. Therefore in Gromacs 4.0 a warning will be generated (and I have added a table in the manual that explains all the possible combinations). If you explicitly define parameters for the A-state, I don't see why you would want the B-parameters to be looked up based on atom-type. You would only want that when the A-state parameters are also determined by the atom type. Berk. From: Maik Goette [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: GMX-mailinglist gmx-users@gromacs.org Subject: [gmx-users] topology treatment in free energy calculations -possible bug Date: Fri, 04 Jan 2008 15:15:57 +0100 Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
parichita parichita wrote: Thaks for your suggesion... I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the problem I encounter is that the pdb2gmx produces the topologies where hydrogens sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. So my questions are; 1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care of hydrogens sitting on carbon atoms in a sugar molecule explicitly? See below, and http://wiki.gromacs.org/index.php/Force_Fields 2- How can I most reliably produce topologies for my disaccharide that will be placed in a water box to perform MD? pdb2gmx... you should find and do some tutorial material to learn about this. I am quite new to MD methods therefore I apologize already now if I put forward something incoherent. You should definitely be doing some background reading of textbooks and tutorials if you haven't yet come across the phenomena of united-atom and all-atom force fields. MD simulations are fabulously easy ways to generate very expensive random numbers, and there's no substitute for library work and careful experimentation. The first few chapters of the GROMACS manual are a good place to start. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Thaks for your suggesion... I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the problem I encounter is that the pdb2gmx produces the topologies where hydrogens sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. So my questions are; 1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care of hydrogens sitting on carbon atoms in a sugar molecule explicitly? 2- How can I most reliably produce topologies for my disaccharide that will be placed in a water box to perform MD? I am quite new to MD methods therefore I apologize already now if I put forward something incoherent. Thanks for the help, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Parichita, My guess is you only thought to have 1-6 linkage, because the atoms seemed so nicely involved in the .pdb file. But you'll have to define a bond explicitly or it won't be there to break in the first place. I think you need to read up on topologies, force fields and general background about simulating molecular systems. Chapter 5 is a must. If you continue on this path, note that sugar dihedrals, especially the ones connecting the rings, are complex. Check out Roberto Lins' paper on the 45a3 force field. Tsjerk On 9/17/07, Mark Abraham wrote: parichita parichita wrote: Hi again. Thank you for your help I found my MANA in the ffG53a5.rtp and i can prepare the .gro and .top file from pdb2gmx. Now , i am facing another problem after solvation of my solute when i run the minimization the 1-6 linkage was broken .. please help me out linkage was broken doesn't help us help you. Please describe in detail what you observed and why you think it was wrong. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Parichita Mazumder Junior Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. - Save all your chat conversations. Find them online.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
parichita parichita wrote: Hi again. Thank you for your help I found my MANA in the ffG53a5.rtp and i can prepare the .gro and .top file from pdb2gmx. Now , i am facing another problem after solvation of my solute when i run the minimization the 1-6 linkage was broken .. please help me out linkage was broken doesn't help us help you. Please describe in detail what you observed and why you think it was wrong. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Parichita, My guess is you only thought to have 1-6 linkage, because the atoms seemed so nicely involved in the .pdb file. But you'll have to define a bond explicitly or it won't be there to break in the first place. I think you need to read up on topologies, force fields and general background about simulating molecular systems. Chapter 5 is a must. If you continue on this path, note that sugar dihedrals, especially the ones connecting the rings, are complex. Check out Roberto Lins' paper on the 45a3 force field. Tsjerk On 9/17/07, Mark Abraham [EMAIL PROTECTED] wrote: parichita parichita wrote: Hi again. Thank you for your help I found my MANA in the ffG53a5.rtp and i can prepare the .gro and .top file from pdb2gmx. Now , i am facing another problem after solvation of my solute when i run the minimization the 1-6 linkage was broken .. please help me out linkage was broken doesn't help us help you. Please describe in detail what you observed and why you think it was wrong. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Just a quick look at the ffG45a3.rtp shows that there is an entry for ADE, however the ADE entry is for Adenine. For help with your problem check out: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database Tom --On Friday, September 14, 2007 14:13:55 +0100 parichita parichita [EMAIL PROTECTED] wrote: Hi, I have facing some problem when converting .pdb file to .gro and .top . I have a .pdb of alpha d-mannose (1-6) alpha d-mannose. I was using the pdb2gmx command and 45a3 forcefield . Showing the fatal error: Atom O in residue ADE 1 not found in rtp entry with 25 atoms while sorting atoms and Warning: 'ADMA' not found in residue topology database, trying to use 'ADE' Warning: 'ADMA' not found in residue topology database, trying to use 'ADE but in ffG45a3.rtp I could not found any ADE ... so I was confused ... Please give me some suggession. The format of my M6M.pdb is, ATOM 1 C5 ADMA1 3.337 1.774 -8.944 1.00 0.00 C ATOM 2 O ADMA1 4.702 1.679 -8.463 1.00 0.00 O ATOM 3 C1 ADMA1 5.227 0.338 -8.248 1.00 0.00 C ATOM 4 C2 ADMA1 4.345 -0.412 -7.222 1.00 0.00 C ATOM 5 O2 ADMA1 4.481 0.211 -5.965 1.00 0.00 O ATOM 6 C3 ADMA1 2.854 -0.372 -7.633 1.00 0.00 C ATOM 7 O3 ADMA1 2.063 -0.925 -6.611 1.00 0.00 O ATOM 8 C4 ADMA1 2.367 1.065 -7.950 1.00 0.00 C ATOM 9 O4 ADMA1 1.062 1.009 -8.476 1.00 0.00 O ATOM 10 C6 ADMA1 3.018 3.281 -9.160 1.00 0.00 C ATOM 11 O6 ADMA1 1.778 3.456 -9.811 1.00 0.00 O ATOM 12 H5 ADMA1 3.271 1.274 -9.929 1.00 0.00 H ATOM 13 H1 ADMA1 6.262 0.415 -7.876 1.00 0.00 H ATOM 14 H2 ADMA1 4.685 -1.464 -7.133 1.00 0.00 H ATOM 15 HO2 ADMA1 5.425 0.166 -5.725 1.00 0.00 H ATOM 16 H3 ADMA1 2.727 -0.987 -8.546 1.00 0.00 H ATOM 17 HO3 ADMA1 1.139 -0.907 -6.925 1.00 0.00 H ATOM 18 H4 ADMA1 2.343 1.645 -7.006 1.00 0.00 H ATOM 19 HO4 ADMA1 0.779 1.926 -8.640 1.00 0.00 H ATOM 20 1H6 ADMA1 3.805 3.735 -9.772 1.00 0.00 H ATOM 21 2H6 ADMA1 3.014 3.809 -8.202 1.00 0.00 H ATOM 22 H6 ADMA1 1.654 4.401 -9.918 1.00 0.00 H ATOM 23 C5 ADMA1B 5.806 -2.519 -10.516 1.00 0.00 C ATOM 24 O ADMA1B 6.529 -3.735 -10.196 1.00 0.00 O ATOM 25 C1 ADMA1B 6.753 -4.668 -11.291 1.00 0.00 C ATOM 26 O1 ADMA1B 7.522 -4.046 -12.268 1.00 0.00 O ATOM 27 C2 ADMA1B 5.398 -5.107 -11.893 1.00 0.00 C ATOM 28 O2 ADMA1B 4.700 -5.870 -10.935 1.00 0.00 O ATOM 29 C3 ADMA1B 4.533 -3.881 -12.271 1.00 0.00 C ATOM 30 O3 ADMA1B 3.254 -4.305 -12.671 1.00 0.00 O ATOM 31 C4 ADMA1B 4.406 -2.866 -11.106 1.00 0.00 C ATOM 32 O4 ADMA1B 3.754 -1.706 -11.569 1.00 0.00 O ATOM 33 C6 ADMA1B 5.743 -1.655 -9.224 1.00 0.00 C ATOM 34 O6 ADMA1B 5.227 -0.368 -9.490 1.00 0.00 O ATOM 35 H5 ADMA1B 6.383 -1.951 -11.270 1.00 0.00 H ATOM 36 H1 ADMA1B 7.300 -5.545 -10.905 1.00 0.00 H ATOM 37 HO1 ADMA1B 7.013 -3.281 -12.602 1.00 0.00 H ATOM 38 H2 ADMA1B 5.572 -5.738 -12.788 1.00 0.00 H ATOM 39 HO2 ADMA1B 5.261 -6.638 -10.719 1.00 0.00 H ATOM 40 H3 ADMA1B 5.014 -3.365 -13.126 1.00 0.00 H ATOM 41 HO3 ADMA1B 2.756 -3.507 -12.928 1.00 0.00 H ATOM 42 H4 ADMA1B 3.788 -3.323 -10.307 1.00 0.00 H ATOM 43 HO4 ADMA1B 3.668 -1.103 -10.809 1.00 0.00 H ATOM 44 1H6 ADMA1B 6.749 -1.553 -8.805 1.00 0.00 H ATOM 45 2H6 ADMA1B 5.131 -2.153 -8.466 1.00 0.00 H TER thanks in advance .. parichita... Parichita Mazumder Junior Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. __ 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology builder
Hi, Is there any fast program to build topology for all-atom OPLS force-field? I tried to use PRODRG, but it only has united atom possibilities. You must either use pdb2gmx or read Chapter 5 and gromacs/share/top/ffoplsaa* and produce one by hand. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] topology doesnt match
Check if you have all group types in your mdp file. Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 From: [EMAIL PROTECTED] on behalf of Robert Selwyne Sent: Mon 4/2/2007 10:40 AM To: gmx-users@gromacs.org Subject: [gmx-users] topology doesnt match Dear GMX users When i tried to rum grompp i get these errors. Would any one be able to sort out this problem? Sincerely Robert - grompp -v -f adp.mdp -po adpmdout.mdp -c genbox.gro -p genbox.top -o gromppout.tpr creating statusfile for 1 node... Back Off! I just backed up adpmdout.mdp to ./#adpmdout.mdp.1# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 WARNING 1 [file genbox.top, line 283]: System has non-zero total charge: -3.00e+00 processing coordinates... Fatal error: number of coordinates in coordinate file (genbox.gro, 3516) does not match topology (genbox.top, 33) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology doesnt match
Robert Selwyne wrote: Dear GMX users When i tried to rum grompp i get these errors. Would any one be able to sort out this problem? Sincerely Robert - grompp -v -f adp.mdp -po adpmdout.mdp -c genbox.gro -p genbox.top -o gromppout.tpr It would be easier to answer your question if you'd told us what you did to generate genbox.gro and genbox.top. As it is, I'm going to have to guess. creating statusfile for 1 node... Back Off! I just backed up adpmdout.mdp to ./#adpmdout.mdp.1# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 WARNING 1 [file genbox.top, line 283]: System has non-zero total charge: -3.00e+00 processing coordinates... Fatal error: number of coordinates in coordinate file (genbox.gro, 3516) does not match topology (genbox.top, 33) I guess that you've added solvent, and not updated the [molecules] section of the .top file. Check chapter 5 of the manual if you don't know how to do this or what I mean :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for D2O
Hi Joys Yu, In addition to Tserks comments you might want to use a more specifically developed heavy water model. Here is a reference you may find usefull: An effective pair potential for heavy water - J. Raul Grigera The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp. 8064-8067. I have created a topology file based on these parameters for a cooperation I did some time back. If you are interested I can email the topology modified FF fiels to you. Regards Andrés El Martes, 27 de Marzo de 2007 03:29, Joys Yu escribió: Dear all, I would like to do simulation of bulk heavy water (D2O). So first thing, I need to get the topology file of D2O. In fact, I would like to use SPC H2O. I just need to change the mass of H in H2O from 1.008 to 2.016. I would like to use gromacs force field(#7). So I revised ffgms.atp. I changed the mass of water hydrogen from 1.008 to 2.016. When I use pdbtogmx to get the topology, it seems fine. I have a bulk heavy water, which has 674 D2O. Here is some of the running results from pdbtogmx: Now there are 674 residues with 2022 atoms Making bonds... Opening library file /home/gromacs-d/share/top/aminoacids.dat Number of bonds was 1348, now 1348 Generating angles, dihedrals and pairs... There are0 dihedrals,0 impropers, 674 angles 0 pairs, 1348 bonds and 0 virtual sites Total mass 13501.164 a.m.u. Total charge 0.000 e The total mass for 674 D2O is correct: 674 * 20.03 = 13501.164 Here is the topology file that I got for D2O: ; ; File 'd2o.top' was generated ; By user: Joys (1002) ; On host: Boyang ; At date: Mon Mar 26 20:15:57 2007 ; ; This is your topology file ; Generated by genbox ; ; Include forcefield parameters #include ffgmx.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Generated by genbox [ molecules ] ; Compound#mols SOL 674 Everything seems fine here. Then I want to do a MD simulation. I used grompp to get the .tpr. I could also run it. But in the .log file, I found the mass of the system is the mass of H2o ( about 12132) not 13501.164. I got D2O topology from pdb2gmx correctly. But it seems that grompp did not read in this topology. Can anybody kindly tell me where the problem is? What should I do to get D2O topology? Many thanks, Joys Yu ___ _ Looking for earth-friendly autos? Browse Top Cars by Green Rating at Yahoo! Autos' Green Center. http://autos.yahoo.com/green_center/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Dr. Andrés N. McCarthy Instituto de Física de Líquidos y Sistemas Biológicos (UNLP-CONICET-CIC) Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata 59-789, CP (1900) La Plata, Argentina Tel: +54-221-4254904 / +54-221-4233283 FAX: +54-221-4257317 e-mail: [EMAIL PROTECTED] web site: www.iflysib.unlp.edu.ar -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology file for D2O
Hi, I am not an expert about heavy water -- but it does seem strange to me to think that you could get heavy water just by changing the mass of the hydrogens in a conventional water model. The *only* thing this will affect is the kinetic energy and mass of water. Presumably changing hydrogen to deuterium *should* also affect other things, such as perhaps slightly altering the electrostatics or dispersion interactions, or the water molecule shape. I'm no expert -- but I bet there's more to it than just a slight change in mass. Maybe you might already know part of the answer to this: Why is it you want to run with D2O instead of regular water? I'm guessing it's because you expect some difference in behavior... Should that really be due exclusively to a difference in mass? David On 3/27/07, Andrés N. McCarthy [EMAIL PROTECTED] wrote: Hi Joys Yu, In addition to Tserks comments you might want to use a more specifically developed heavy water model. Here is a reference you may find usefull: An effective pair potential for heavy water - J. Raul Grigera The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp. 8064-8067. I have created a topology file based on these parameters for a cooperation I did some time back. If you are interested I can email the topology modified FF fiels to you. Regards Andrés El Martes, 27 de Marzo de 2007 03:29, Joys Yu escribió: Dear all, I would like to do simulation of bulk heavy water (D2O). So first thing, I need to get the topology file of D2O. In fact, I would like to use SPC H2O. I just need to change the mass of H in H2O from 1.008 to 2.016. I would like to use gromacs force field(#7). So I revised ffgms.atp. I changed the mass of water hydrogen from 1.008 to 2.016. When I use pdbtogmx to get the topology, it seems fine. I have a bulk heavy water, which has 674 D2O. Here is some of the running results from pdbtogmx: Now there are 674 residues with 2022 atoms Making bonds... Opening library file /home/gromacs-d/share/top/aminoacids.dat Number of bonds was 1348, now 1348 Generating angles, dihedrals and pairs... There are0 dihedrals,0 impropers, 674 angles 0 pairs, 1348 bonds and 0 virtual sites Total mass 13501.164 a.m.u. Total charge 0.000 e The total mass for 674 D2O is correct: 674 * 20.03 = 13501.164 Here is the topology file that I got for D2O: ; ; File 'd2o.top' was generated ; By user: Joys (1002) ; On host: Boyang ; At date: Mon Mar 26 20:15:57 2007 ; ; This is your topology file ; Generated by genbox ; ; Include forcefield parameters #include ffgmx.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Generated by genbox [ molecules ] ; Compound#mols SOL 674 Everything seems fine here. Then I want to do a MD simulation. I used grompp to get the .tpr. I could also run it. But in the .log file, I found the mass of the system is the mass of H2o ( about 12132) not 13501.164. I got D2O topology from pdb2gmx correctly. But it seems that grompp did not read in this topology. Can anybody kindly tell me where the problem is? What should I do to get D2O topology? Many thanks, Joys Yu ___ _ Looking for earth-friendly autos? Browse Top Cars by Green Rating at Yahoo! Autos' Green Center. http://autos.yahoo.com/green_center/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Dr. Andrés N. McCarthy Instituto de Física de Líquidos y Sistemas Biológicos (UNLP-CONICET-CIC) Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata 59-789, CP (1900) La Plata, Argentina Tel: +54-221-4254904 / +54-221-4233283 FAX: +54-221-4257317 e-mail: [EMAIL PROTECTED] web site: www.iflysib.unlp.edu.ar -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read
