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/**
[gmx-users] Topology file-residue unknown
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 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? 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. Is there something wrong with my rtp? Could I trouble you to let me know what wrong is? -- Thanks, J. N. -- 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 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
