Re: [gmx-users] Diagnosing + system blowing up
I edited the grompp output and sent it to you. Bring that again here: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations ERROR 1 [file topol.top, line 414]: No default Bond types ERROR 2 [file topol.top, line 1698]: No default U-B types ERROR 3 [file topol.top, line 1699]: No default U-B types ERROR 4 [file topol.top, line 2345]: No default Proper Dih. types ERROR 5 [file topol.top, line 2346]: No default Proper Dih. types ERROR 6 [file topol.top, line 3278]: No default Improper Dih. types And wrote line 414 is : line 414 of topol.tp: [bonds] 1 2 1 Sincerely, Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Tuesday, July 31, 2012 4:40 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 31/07/2012 7:16 AM, Shima Arasteh wrote: > Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) > > I regenerated the topol.top to check the correctness of input and FF files. > Some output has been changed however a little bit. Now, I bring you all was > needed again: > >> 1. rtp entry >> >> [ FVAL ] > [ atoms ] > CN C 0.357 0 > ON O -0.51 1 > H1 HA 0.100 2 > N NH1 -0.423 3 > HN H 0.333 4 > CA CT1 0.034 5 > HA HB 0.09 6 > CB CT1 -0.093 7 > HB HA 0.09 8 > CG1 CT3 -0.268 9 > HG11 HA 0.09 10 > HG12 HA 0.09 11 > HG13 HA 0.09 12 > CG2 CT3 -0.268 13 > HG21 HA 0.09 14 > HG22 HA 0.09 15 > HG23 HA 0.09 16 > C C 0.528 17 > O O -0.510 18 > [ bonds ] > CN H1 > CN ON > CN N > N HN > CA N > CA HA > CA C > C O > CA CB > CB HB > CB CG1 > CB CG2 > CG2 HG21 > CG2 HG22 > CG2 HG23 > CG1 HG11 > CG1 HG12 > CG1 HG13 > > [ impropers ] > CN N ON H1 > >> 2. hdb entry > In which file? > *aminoacids.hdb > > >> FVAL 6 >> 1 1 H1 CN N ON > This should be generating H1 bonded to CN... > >> 1 1 HN N C CA >> 1 5 HA CA N C CB >> 1 5 HB CB CA CG1 CG2 >> 3 4 HG1 CG1 CB CA >> 3 4 HG2 CG2 CB CA >> >> 3. N-terminal fragment >> HETATM 1 CN FVAL 1 -0.721 1.600 1.249 >> HETATM 2 ON FVAL 1 -0.839 2.806 1.453 >> ATOM 3 N FVAL 1 -1.227 0.728 2.125 >> ATOM 4 CA FVAL 1 -1.918 1.159 3.323 >> ATOM 5 C FVAL 1 -1.969 2.678 3.410 >> ATOM 6 O FVAL 1 -0.931 3.335 3.447 >> ATOM 7 CB FVAL 1 -1.219 0.644 4.576 >> ATOM 8 CG1 FVAL 1 0.208 1.178 4.618 >> ATOM 9 CG2 FVAL 1 -1.976 1.118 5.812 >> >> 4. pdb2gmx command >> #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter >> >> 5. pdb2gmx output > Using the Charmm36-modified force field in directory ./charmm36-modified.ff > > Opening force field file ./charmm36-modified.ff/aminoacids.r2b > Opening force field file ./charmm36-modified.ff/rna.r2b > Reading monomer.pdb... > Read 177 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 1 chains and 0 blocks of water and 24 residues with 177 atoms > > chain #res #atoms > 1 ' ' 24 177 > > All occupancy fields zero. This is probably not an X-Ray structure > Opening force field file ./charmm36-modified.ff/atomtypes.atp > Atomtype 1 > Reading residue database... (charmm36-modified) > Opening force field file ./charmm36-modified.ff/aminoacids.rtp > Residue 42 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/dna.rtp > Residue 46 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/lipids.rtp > Residue 82 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/rna.rtp > Residue 86 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/aminoacids.hdb > Opening force field file ./charmm36-modified.ff/dna.hdb > Opening force field file ./charmm36-modified.ff/lipids.hdb > Opening force field file ./charmm36-modified.ff/rna.hdb > Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb > Opening force field file ./charmm36-modified.ff/dna.n.tdb > Opening force field file ./charmm36-modified.ff/rna.n.tdb > Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb > Opening force field file ./charmm36-modified.ff/dna.c.tdb > Opening force field file ./charmm36-modified.ff/rna.c.tdb > > Back Off! I just backed up topol.top to ./#topol.top.2# > Processing chain 1 (177 atom
Re: [gmx-users] Diagnosing + system blowing up
On 31/07/2012 7:16 AM, Shima Arasteh wrote: Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) I regenerated the topol.top to check the correctness of input and FF files. Some output has been changed however a little bit. Now, I bring you all was needed again: 1. rtp entry [ FVAL ] [ atoms ] CNC 0.3570 ONO-0.511 H1HA0.1002 NNH1-0.4233 HNH0.3334 CACT10.0345 HAHB0.096 CBCT1-0.0937 HBHA0.098 CG1CT3-0.2689 HG11HA0.0910 HG12HA0.0911 HG13HA0.0912 CG2CT3-0.26813 HG21HA0.0914 HG22HA0.0915 HG23HA0.0916 CC0.52817 OO-0.51018 [ bonds ] CNH1 CNON CNN NHN CAN CAHA CAC CO CACB CBHB CBCG1 CBCG2 CG2HG21 CG2HG22 CG2HG23 CG1HG11 CG1HG12 CG1HG13 [ impropers ] CN NONH1 2. hdb entry In which file? *aminoacids.hdb FVAL6 11H1CNNON This should be generating H1 bonded to CN... 11HNNCCA 15HACANCCB 15HBCBCACG1CG2 34HG1CG1CBCA 34HG2CG2CBCA 3. N-terminal fragment HETATM1 CN FVAL1 -0.721 1.600 1.249 HETATM2 ON FVAL1 -0.839 2.806 1.453 ATOM 3 N FVAL1 -1.227 0.728 2.125 ATOM 4 CA FVAL1 -1.918 1.159 3.323 ATOM 5 C FVAL1 -1.969 2.678 3.410 ATOM 6 O FVAL1 -0.931 3.335 3.447 ATOM 7 CB FVAL1 -1.219 0.644 4.576 ATOM 8 CG1 FVAL1 0.208 1.178 4.618 ATOM 9 CG2 FVAL1 -1.976 1.118 5.812 4. pdb2gmx command #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 5. pdb2gmx output Using the Charmm36-modified force field in directory ./charmm36-modified.ff Opening force field file ./charmm36-modified.ff/aminoacids.r2b Opening force field file ./charmm36-modified.ff/rna.r2b Reading monomer.pdb... Read 177 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 24 residues with 177 atoms chain #res #atoms 1 ' '24177 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./charmm36-modified.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36-modified) Opening force field file ./charmm36-modified.ff/aminoacids.rtp Residue 42 Sorting it all out... Opening force field file ./charmm36-modified.ff/dna.rtp Residue 46 Sorting it all out... Opening force field file ./charmm36-modified.ff/lipids.rtp Residue 82 Sorting it all out... Opening force field file ./charmm36-modified.ff/rna.rtp Residue 86 Sorting it all out... Opening force field file ./charmm36-modified.ff/aminoacids.hdb Opening force field file ./charmm36-modified.ff/dna.hdb Opening force field file ./charmm36-modified.ff/lipids.hdb Opening force field file ./charmm36-modified.ff/rna.hdb Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb Opening force field file ./charmm36-modified.ff/dna.n.tdb Opening force field file ./charmm36-modified.ff/rna.n.tdb Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb Opening force field file ./charmm36-modified.ff/dna.c.tdb Opening force field file ./charmm36-modified.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 (177 atoms, 24 residues) Identified residue FVAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for FVAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus FVAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: CT2 3: CT3 4: None 0 End terminus GLY-24: COO- Opening force field file ./charmm36-modified.ff/aminoacids.arn Opening force field file ./charmm36-modified.ff/dna.arn Opening force field file ./charmm36-modified.ff/rna.arn Checking for duplicate atoms Now there are 24 residues with 360 atoms Making bonds... Number of bonds was 362, now 362 Generating angles, dihedrals and pairs... Before cleaning: 925 pairs Before cleaning: 930 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 22 cmap torsion pairs There are 930 dihedrals, 49 impropers, 644 angles 916 pairs, 362 bonds and 0 virtual sites Total mass 2510.906 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.1# Writing coordinate file... Back Off! I just backed up monomer.gro to ./#monomer.gro.1#
Re: [gmx-users] Linear Interaction energy calculations
On 7/30/12 5:15 PM, sai nitin wrote: Dear all, I recently started protein ligand simulation using gromacs my aim is to calculate binding free energies after simulations...I adapted justin tutorial and done 10 ns MD simulations using CHARMM FF and now going through LIE (Linear Interaction Energie method) g_lie in gromacs.. And came across that to perform LIE using gromacs involves two MD simulations one with protein - ligand simulation in solvent (which i finished)..and another with ligand only in solution in this step i got stuck can any body tell or suggest some tutorials to perform MD simulations for only ligand It's nothing more than a simulation of a solute in water. Prepare a coordinate file of the ligand, solvate in some suitable box, and proceed. If you're already run a simulation of a protein in complex with the ligand, then you have the ligand's topology. From that, construction of a .top is trivial, i.e.: #include "whatever.ff/forcefield.itp" #include "ligand.itp" #include "whatever.ff/whatever_water_model.itp" #include "whatever.ff/ions.itp" [ system ] ligand in water [ molecules ] LIG 1 SOL X (ions if necessary) -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] About EM Error (simulation exploding)
On 7/30/12 1:07 PM, vidhya sankar wrote: Dear Justin, Thank you for your Previous Reply. I have got the following Error in EM using steepest Descent method in gromacs Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is larger than the 1-4 table size 3.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size If energy minimization fails, then there is something unphysical about the starting geometry that cannot be resolved. Note that 3.0 nm is a very long distance for a normal 1-4 interactions. What are these atoms and why are they linked by 3 bonds? I know That my System is exploding .I have checked that my ouput .gro file in VMD there is No error . in my system. Then What KInd of Physical Parameter lead to error My box size is ./editconf_d -f 1OG2O.gro -o 1OG2Onewbox1.gro-center 7.0 8.0 7.0 -box 14.0 16.0 14.0 my Em.mdp file as follows integrator = steep emtol = 1000 emstep = 0.01 constraints = none nsteps = 5 nstlist = 1 ns_type = grid rlist = 2.0 coulombtype = PME rcoulomb= 2.0 rvdw= 2.0 pbc = xyz The cutoff values seem arbitrary. There is no force field in Gromacs that uses 2.0 nm for short-range nonbonded cutoffs. -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] Diagnosing + system blowing up
Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) I regenerated the topol.top to check the correctness of input and FF files. Some output has been changed however a little bit. Now, I bring you all was needed again: > 1. rtp entry > >[ FVAL ] [ atoms ] CN C 0.357 0 ON O -0.51 1 H1 HA 0.100 2 N NH1 -0.423 3 HN H 0.333 4 CA CT1 0.034 5 HA HB 0.09 6 CB CT1 -0.093 7 HB HA 0.09 8 CG1 CT3 -0.268 9 HG11 HA 0.09 10 HG12 HA 0.09 11 HG13 HA 0.09 12 CG2 CT3 -0.268 13 HG21 HA 0.09 14 HG22 HA 0.09 15 HG23 HA 0.09 16 C C 0.528 17 O O -0.510 18 [ bonds ] CN H1 CN ON CN N N HN CA N CA HA CA C C O CA CB CB HB CB CG1 CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 CG1 HG11 CG1 HG12 CG1 HG13 [ impropers ] CN N ON H1 > 2. hdb entry In which file? *aminoacids.hdb > FVAL 6 > 1 1 H1 CN N ON This should be generating H1 bonded to CN... > 1 1 HN N C CA > 1 5 HA CA N C CB > 1 5 HB CB CA CG1 CG2 > 3 4 HG1 CG1 CB CA > 3 4 HG2 CG2 CB CA > > 3. N-terminal fragment > HETATM 1 CN FVAL 1 -0.721 1.600 1.249 > HETATM 2 ON FVAL 1 -0.839 2.806 1.453 > ATOM 3 N FVAL 1 -1.227 0.728 2.125 > ATOM 4 CA FVAL 1 -1.918 1.159 3.323 > ATOM 5 C FVAL 1 -1.969 2.678 3.410 > ATOM 6 O FVAL 1 -0.931 3.335 3.447 > ATOM 7 CB FVAL 1 -1.219 0.644 4.576 > ATOM 8 CG1 FVAL 1 0.208 1.178 4.618 > ATOM 9 CG2 FVAL 1 -1.976 1.118 5.812 > > 4. pdb2gmx command > #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter > > 5. pdb2gmx output Using the Charmm36-modified force field in directory ./charmm36-modified.ff Opening force field file ./charmm36-modified.ff/aminoacids.r2b Opening force field file ./charmm36-modified.ff/rna.r2b Reading monomer.pdb... Read 177 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 24 residues with 177 atoms chain #res #atoms 1 ' ' 24 177 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./charmm36-modified.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36-modified) Opening force field file ./charmm36-modified.ff/aminoacids.rtp Residue 42 Sorting it all out... Opening force field file ./charmm36-modified.ff/dna.rtp Residue 46 Sorting it all out... Opening force field file ./charmm36-modified.ff/lipids.rtp Residue 82 Sorting it all out... Opening force field file ./charmm36-modified.ff/rna.rtp Residue 86 Sorting it all out... Opening force field file ./charmm36-modified.ff/aminoacids.hdb Opening force field file ./charmm36-modified.ff/dna.hdb Opening force field file ./charmm36-modified.ff/lipids.hdb Opening force field file ./charmm36-modified.ff/rna.hdb Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb Opening force field file ./charmm36-modified.ff/dna.n.tdb Opening force field file ./charmm36-modified.ff/rna.n.tdb Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb Opening force field file ./charmm36-modified.ff/dna.c.tdb Opening force field file ./charmm36-modified.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 (177 atoms, 24 residues) Identified residue FVAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for FVAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus FVAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: CT2 3: CT3 4: None 0 End terminus GLY-24: COO- Opening force field file ./charmm36-modified.ff/aminoacids.arn Opening force field file ./charmm36-modified.ff/dna.arn Opening force field file ./charmm36-modified.ff/rna.arn Checking for duplicate atoms Now there are 24 residues with 360 atoms Making bonds... Number of bonds was 362, now 362 Generating angles, dihedrals and pairs... Before cleaning: 925 pairs Before cleaning: 930 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 22 cmap torsion pairs There are 930 dihedrals, 49 impropers, 644 angles 916 pairs, 362 bonds and 0 virtual sites Total mass 2510.906 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.1# Writing coordinate file... Back Off! I just backed up monomer.gro to ./#monomer.gro.1# - PLEASE NOTE You have
[gmx-users] Linear Interaction energy calculations
Dear all, I recently started protein ligand simulation using gromacs my aim is to calculate binding free energies after simulations...I adapted justin tutorial and done 10 ns MD simulations using CHARMM FF and now going through LIE (Linear Interaction Energie method) g_lie in gromacs.. And came across that to perform LIE using gromacs involves two MD simulations one with protein - ligand simulation in solvent (which i finished)..and another with ligand only in solution in this step i got stuck can any body tell or suggest some tutorials to perform MD simulations for only ligand Thanks in advance -- Sainitin D -- 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] About EM Error (simulation exploding)
Dear Justin, Thank you for your Previous Reply. I have got the following Error in EM using steepest Descent method in gromacs Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is larger than the 1-4 table size 3.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I know That my System is exploding .I have checked that my ouput .gro file in VMD there is No error . in my system. Then What KInd of Physical Parameter lead to error My box size is ./editconf_d -f 1OG2O.gro -o 1OG2Onewbox1.gro -center 7.0 8.0 7.0 -box 14.0 16.0 14.0 my Em.mdp file as follows integrator = steep emtol = 1000 emstep = 0.01 constraints = none nsteps = 5 nstlist = 1 ns_type = grid rlist = 2.0 coulombtype = PME rcoulomb = 2.0 rvdw = 2.0 pbc = xyz Is there is any contradiction. between box Size and .mdp parameters I am sure There is No error in .top and .gro file Then what could be the Source of error Thanks in Advance With Regards S.Vidhyasankar -- 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] Diagnosing + system blowing up
On 30/07/2012 8:49 PM, Shima Arasteh wrote: If you want further help, you will need to paste your .rtp entry(s), the N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp >command line, and full grompp output. You may think your context is clear, but nobody else is paying your problem as much attention as you are. I won't help further if you only provide partial information. 1. rtp entry [ FVAL ] [ atoms ] CNC 0.3570 ONO-0.511 H1HA0.1002 NNH1-0.4233 HNH0.3334 CACT10.0345 HAHB0.096 CBCT1-0.0937 HBHA0.098 CG1CT3-0.2689 HG11HA0.0910 HG12HA0.0911 HG13HA0.0912 CG2CT3-0.26813 HG21HA0.0914 HG22HA0.0915 HG23HA0.0916 CC0.52817 OO-0.51018 [ bonds ] CNH1 CNON CNN NHN CAN CAHA CAC CO CACB CBHB CBCG1 CBCG2 CG2HG21 CG2HG22 CG2HG23 CG1HG11 CG1HG12 CG1HG13grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr [ impropers ] CN NONH1 2. hdb entry In which file? FVAL6 11H1CNNON This should be generating H1 bonded to CN... 11HNNCCA 15HACANCCB 15HBCBCACG1CG2 34HG1CG1CBCA 34HG2CG2CBCA 3. N-terminal fragment HETATM1 CN FVAL1 -0.721 1.600 1.249 HETATM2 ON FVAL1 -0.839 2.806 1.453 ATOM 3 N FVAL1 -1.227 0.728 2.125 ATOM 4 CA FVAL1 -1.918 1.159 3.323 ATOM 5 C FVAL1 -1.969 2.678 3.410 ATOM 6 O FVAL1 -0.931 3.335 3.447 ATOM 7 CB FVAL1 -1.219 0.644 4.576 ATOM 8 CG1 FVAL1 0.208 1.178 4.618 ATOM 9 CG2 FVAL1 -1.976 1.118 5.812 4. pdb2gmx command #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 5. pdb2gmx output Using the Charmm36-modified force field in directory ./charmm36-modified.ff Opening force field file ./charmm36-modified.ff/aminoacids.r2b Opening force field file ./charmm36-modified.ff/rna.r2b Reading monomer.pdb... Read 177 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 24 residues with 177 atoms chain #res #atoms 1 ' '24177 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./charmm36-modified.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36-modified) Opening force field file ./charmm36-modified.ff/aminoacids.rtp Residue 42 Sorting it all out... Opening force field file ./charmm36-modified.ff/dna.rtp Residue 46 Sorting it all out... Opening force field file ./charmm36-modified.ff/lipids.rtp Residue 82 Sorting it all out... Opening force field file ./charmm36-modified.ff/rna.rtp Residue 86 Sorting it all out... Opening force field file ./charmm36-modified.ff/aminoacids.hdb ... and here's your .hdb file being picked up (and pdb2gmx must have found definitions for building hydrogens for FVAL somehow)... Opening force field file ./charmm36-modified.ff/dna.hdb Opening force field file ./charmm36-modified.ff/lipids.hdb Opening force field file ./charmm36-modified.ff/rna.hdb Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb Opening force field file ./charmm36-modified.ff/dna.n.tdb Opening force field file ./charmm36-modified.ff/rna.n.tdb Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb Opening force field file ./charmm36-modified.ff/dna.c.tdb Opening force field file ./charmm36-modified.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.1# Processing chain 1 (177 atoms, 24 residues) Identified residue FVAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for FVAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus FVAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: CT2 3: CT3 4: None 0 End terminus GLY-24: COO- Opening force field file ./charmm36-modified.ff/aminoacids.arn Opening force field file ./charmm36-modified.ff/dna.arn Opening force field file ./charmm36-modified.ff/rna.arn Checking for duplicate atoms Now there are 24 residues with 360 atoms Making bonds... Warning: Long Bond (1-18 = 0.357049 nm) ...but H1 is built as atom 18 and too far away... Number of bonds was 361, now 361 Generating angles, dihedrals and pairs... Before cleani
Re: [gmx-users] Gromacs installation
Thank you M.ark.. I got following reply.. Fatal error : mdrun -multi is not supported with thread library .Please compile gromacs with MPI support. I have to try to compile gromacs as per the webpage instructions... With best wishes and regards.. Rama David.. -- 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] Gromacs installation
On 30/07/2012 8:34 PM, rama david wrote: thank you for immediate reply... Suppose, If I installed from Fedora software packages How to check that Gromacs installed in Parallel version and can performed REMD Make topol0.tpr and topol1.tpr as copies of the same .tpr file, and run mpirun mdrun_mpi -multi 2 -replex 10 It won't do REMD, but it'll complain about the temperatures being the same, which serves to test that REMD will work. Or just set up a proper REMD system and try it. See manual and webpage advice. Mark -- 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] Diagnosing + system blowing up
>If you want further help, you will need to paste your .rtp entry(s), the >N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full >pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp >>command line, and full grompp output. You may think your context is clear, >but nobody else is paying your problem as much attention as you are. I won't >help further if you only provide partial information. 1. rtp entry [ FVAL ] [ atoms ] CN C 0.357 0 ON O -0.51 1 H1 HA 0.100 2 N NH1 -0.423 3 HN H 0.333 4 CA CT1 0.034 5 HA HB 0.09 6 CB CT1 -0.093 7 HB HA 0.09 8 CG1 CT3 -0.268 9 HG11 HA 0.09 10 HG12 HA 0.09 11 HG13 HA 0.09 12 CG2 CT3 -0.268 13 HG21 HA 0.09 14 HG22 HA 0.09 15 HG23 HA 0.09 16 C C 0.528 17 O O -0.510 18 [ bonds ] CN H1 CN ON CN N N HN CA N CA HA CA C C O CA CB CB HB CB CG1 CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 CG1 HG11 CG1 HG12 CG1 HG13grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr [ impropers ] CN N ON H1 2. hdb entry FVAL 6 1 1 H1 CN N ON 1 1 HN N C CA 1 5 HA CA N C CB 1 5 HB CB CA CG1 CG2 3 4 HG1 CG1 CB CA 3 4 HG2 CG2 CB CA 3. N-terminal fragment HETATM 1 CN FVAL 1 -0.721 1.600 1.249 HETATM 2 ON FVAL 1 -0.839 2.806 1.453 ATOM 3 N FVAL 1 -1.227 0.728 2.125 ATOM 4 CA FVAL 1 -1.918 1.159 3.323 ATOM 5 C FVAL 1 -1.969 2.678 3.410 ATOM 6 O FVAL 1 -0.931 3.335 3.447 ATOM 7 CB FVAL 1 -1.219 0.644 4.576 ATOM 8 CG1 FVAL 1 0.208 1.178 4.618 ATOM 9 CG2 FVAL 1 -1.976 1.118 5.812 4. pdb2gmx command #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 5. pdb2gmx output Using the Charmm36-modified force field in directory ./charmm36-modified.ff Opening force field file ./charmm36-modified.ff/aminoacids.r2b Opening force field file ./charmm36-modified.ff/rna.r2b Reading monomer.pdb... Read 177 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 24 residues with 177 atoms chain #res #atoms 1 ' ' 24 177 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./charmm36-modified.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36-modified) Opening force field file ./charmm36-modified.ff/aminoacids.rtp Residue 42 Sorting it all out... Opening force field file ./charmm36-modified.ff/dna.rtp Residue 46 Sorting it all out... Opening force field file ./charmm36-modified.ff/lipids.rtp Residue 82 Sorting it all out... Opening force field file ./charmm36-modified.ff/rna.rtp Residue 86 Sorting it all out... Opening force field file ./charmm36-modified.ff/aminoacids.hdb Opening force field file ./charmm36-modified.ff/dna.hdb Opening force field file ./charmm36-modified.ff/lipids.hdb Opening force field file ./charmm36-modified.ff/rna.hdb Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb Opening force field file ./charmm36-modified.ff/dna.n.tdb Opening force field file ./charmm36-modified.ff/rna.n.tdb Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb Opening force field file ./charmm36-modified.ff/dna.c.tdb Opening force field file ./charmm36-modified.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.1# Processing chain 1 (177 atoms, 24 residues) Identified residue FVAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for FVAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus FVAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: CT2 3: CT3 4: None 0 End terminus GLY-24: COO- Opening force field file ./charmm36-modified.ff/aminoacids.arn Opening force field file ./charmm36-modified.ff/dna.arn Opening force field file ./charmm36-modified.ff/rna.arn Checking for duplicate atoms Now there are 24 residues with 360 atoms Making bonds... Warning: Long Bond (1-18 = 0.357049 nm) Number of bonds was 361, now 361 Generating angles, dihedrals and pairs... Before cleaning: 920 pairs Before cleaning: 925 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 22 cmap torsion pairs There are 925 dihedrals, 49 impropers, 642 angles 911 pairs, 361 bonds and 0 virtual sites Total mass 2510.906 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.it
Re: [gmx-users] Gromacs installation
thank you for immediate reply... Suppose, If I installed from Fedora software packages How to check that Gromacs installed in Parallel version and can performed REMD Thank you in Advance.. -- 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] a problem using g_sgangle
On 7/30/12 5:55 AM, Za Pour wrote: Dear gmx users I am trying to analyze the results of my simulations. a system including one CNT+12 small molecules.I would like to know the distribution of angles formed by these 12 small molecules around CNT.I have found from manual that g_sgangle may do that however, in the manual has been said that groups in this program are defined by a number of atoms given in an index file and may be two or three atoms in size. but my small molecule has 60 atoms.would you please tell me is there any way I can solve the problem. Your index file has to contain atoms for which an angle can be measured. It can't contain all 60 atoms per molecule. An identical question was posted just 2 or 3 days ago; please have a look in the list archive to find the suggestions posted in that thread. -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
[gmx-users] a problem using g_sgangle
Dear gmx users I am trying to analyze the results of my simulations. a system including one CNT+12 small molecules.I would like to know the distribution of angles formed by these 12 small molecules around CNT.I have found from manual that g_sgangle may do that however, in the manual has been said that groups in this program are defined by a number of atoms given in an index file and may be two or three atoms in size. but my small molecule has 60 atoms.would you please tell me is there any way I can solve the problem. thanks in advance -- 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] Diagnosing + system blowing up
On 30/07/2012 7:41 PM, Shima Arasteh wrote: You are right, CT1 is incorrect for sure. But the other option is C(carbonyl C) . Maybe I couldn't say it clearly. The FVAL which I sent before through mailing list, is the result of this formamide and the CGenff generation: [ FVAL ] [ atoms ] CNC0.3570 ONO-0.511 H1HA0.1002 NNH1-0.4233 HNH0.3334 CACT10.0345 HAHB0.096 CBCT1-0.0937 HBHA0.098 CG1CT3-0.2689 HG11HA0.0910 HG12HA0.0911 HG13HA0.0912 CG2CT3-0.26813 HG21HA0.0914 HG22HA0.0915 HG23HA0.0916 CC0.52817 OO-0.51018 [ bonds ] CNH1 CNON CNN NH CAN CAHA CAC CO CACB CBHB CBCG1 CBCG2 CG2HG21 CG2HG22 CG2HG23 CG1HG11 CG1HG12 CG1HG13 [ impropers ] CN NONH1 This is the new residue which I defined and sent you(as remember), I used these parameters and atomtypes , and then went through mailing list and asked for your help a few days ago. All over , with this procedure , I couldn't get the an acceptable result. You say you've chosen suitable atom types. grompp says it can't find parameters for interactions using them. So until you find out further information, you don't have suitable atom types. I've said all I have to say until you go and look up whether the bonds, angles and dihedrals that you want to use are defined in your force field for the atom types you want to use. If you want further help, you will need to paste your .rtp entry(s), the N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp command line, and full grompp output. You may think your context is clear, but nobody else is paying your problem as much attention as you are. I won't help further if you only provide partial information. Mark -- 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] Diagnosing + system blowing up
You are right, CT1 is incorrect for sure. But the other option is C(carbonyl C) . Maybe I couldn't say it clearly. The FVAL which I sent before through mailing list, is the result of this formamide and the CGenff generation: [ FVAL ] >> [ atoms ] >> CN C 0.357 0 >> ON O -0.51 1 >> H1 HA 0.100 2 >> N NH1 -0.423 3 >> HN H 0.333 4 >> CA CT1 0.034 5 >> HA HB 0.09 6 >> CB CT1 -0.093 7 >> HB HA 0.09 8 >> CG1 CT3 -0.268 9 >> HG11 HA 0.09 10 >> HG12 HA 0.09 11 >> HG13 HA 0.09 12 >> CG2 CT3 -0.268 13 >> HG21 HA 0.09 14 >> HG22 HA 0.09 15 >> HG23 HA 0.09 16 >> C C 0.528 17 >> O O -0.510 18 >> [ bonds ] >> CN H1 >> CN ON >> CN N >> N H >> CA N >> CA HA >> CA C >> C O >> CA CB >> CB HB >> CB CG1 >> CB CG2 >> CG2 HG21 >> CG2 HG22 >> CG2 HG23 >> CG1 HG11 >> CG1 HG12 >> CG1 HG13 >> >> [ impropers ] >> CN N ON H1 This is the new residue which I defined and sent you(as remember), I used these parameters and atomtypes , and then went through mailing list and asked for your help a few days ago. All over , with this procedure , I couldn't get the an acceptable result. Sincerely, Shima - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Monday, July 30, 2012 1:51 PM Subject: Re: [gmx-users] Diagnosing + system blowing up On 30/07/2012 7:11 PM, Shima Arasteh wrote: > In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of > formyl group ( as you see earlier) No, I saw atom types chosen that included wrong things like CT1. If you're happy that you're using atom types that belong in formyl, then go and do the rest of the investigative procedure I suggested for the bonds/angles/dihedrals. I'm not going to write it again! > . If I don't use these, so what atom types?! > I sent an email to Prof.Roux the author of this article > http://www.pnas.org/content/101/1/117.abstract . He suggested me to use the > parameters of formamide the charmm36.rtf file . > RESI FORM 0.00 ! CH3NO formamide, adm jr. > GROUP > ATOM HA HGR52 0.08 ! > ATOM C CG2O1 0.42 ! O Hc > ATOM N NG2S2 -0.69 ! \\ / > ATOM HC HGP1 0.35 ! C--N > ATOM HT HGP1 0.35 ! / \ > ATOM O OG2D1 -0.51 ! HA Ht > > I found something similar to what I used here for my defined formyl > group.Would this be useful? Potentially a good start, but you will have to decide how to deal with the charge distribution, because you need to replace Ht with the rest of valine and end up with a neutral charge distribution that makes sense. One approach is to define a residue (based on those atom types and charges) with just formyl, since the above fragment has HC(O)- that is almost neutral. You can then proceed with using normal valine after that. Mark > > Sincerely, > Shima > > > - Original Message - > From: Mark Abraham > To: Discussion list for GROMACS users > Cc: > Sent: Monday, July 30, 2012 1:22 PM > Subject: Re: [gmx-users] Diagnosing + system blowing up > > On 30/07/2012 6:36 PM, Shima Arasteh wrote: >> Thanks dear Mark. >> Actually the atomtype C is more suitable for C atom of formyl and not CT1! >> >> The same as before I get the no default bonds/angles/dihedral errors . You >> explained what I am suppose. >> I can understand the way of matching the coordinate file and atom types in >> .rtp file. But it's not clear for me that what I am supposed to check? >> bonds? I don't know what I need to do. > Your .rtp entry has to specify atom types. Those atom types have to make > chemical sense. Then there have to be bond/angle/dihedral parameters for all > the combinations you want to use. It may be that this is impossible (and > pdb2gmx is having trouble, which suggests this is true), but you can't know > without looking at the force field files. This is about the third time I've > said to go looking for formyl atom types in atomtypes.atp. They're probably > not there. Atom types for HC(O)N(H)R... are almost certainly not there, and > they are what you really want, and they'd be quite different from HC(O)R > formyl anyway. > >> If I look for the bonds/dihedrals and then don't find them, what's the next >> step? > Search the literature to see if anyone else has used this functional group, > but probably give up and use acetyl, like everybody else does. You have to > have a compelling reason to want to bother to parameterize this group, and > I'd suggest you get a lot more experience first. > > Mark >
Re: [gmx-users] Diagnosing + system blowing up
On 30/07/2012 7:11 PM, Shima Arasteh wrote: In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of formyl group ( as you see earlier) No, I saw atom types chosen that included wrong things like CT1. If you're happy that you're using atom types that belong in formyl, then go and do the rest of the investigative procedure I suggested for the bonds/angles/dihedrals. I'm not going to write it again! . If I don't use these, so what atom types?! I sent an email to Prof.Roux the author of this article http://www.pnas.org/content/101/1/117.abstract . He suggested me to use the parameters of formamide the charmm36.rtf file . RESI FORM 0.00 ! CH3NO formamide, adm jr. GROUP ATOM HA HGR520.08 ! ATOM CCG2O10.42 ! O Hc ATOM NNG2S2 -0.69 ! \\ / ATOM HC HGP1 0.35 ! C--N ATOM HT HGP1 0.35 ! /\ ATOM OOG2D1 -0.51 ! HA Ht I found something similar to what I used here for my defined formyl group.Would this be useful? Potentially a good start, but you will have to decide how to deal with the charge distribution, because you need to replace Ht with the rest of valine and end up with a neutral charge distribution that makes sense. One approach is to define a residue (based on those atom types and charges) with just formyl, since the above fragment has HC(O)- that is almost neutral. You can then proceed with using normal valine after that. Mark Sincerely, Shima - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Monday, July 30, 2012 1:22 PM Subject: Re: [gmx-users] Diagnosing + system blowing up On 30/07/2012 6:36 PM, Shima Arasteh wrote: Thanks dear Mark. Actually the atomtype C is more suitable for C atom of formyl and not CT1! The same as before I get the no default bonds/angles/dihedral errors . You explained what I am suppose. I can understand the way of matching the coordinate file and atom types in .rtp file. But it's not clear for me that what I am supposed to check? bonds? I don't know what I need to do. Your .rtp entry has to specify atom types. Those atom types have to make chemical sense. Then there have to be bond/angle/dihedral parameters for all the combinations you want to use. It may be that this is impossible (and pdb2gmx is having trouble, which suggests this is true), but you can't know without looking at the force field files. This is about the third time I've said to go looking for formyl atom types in atomtypes.atp. They're probably not there. Atom types for HC(O)N(H)R... are almost certainly not there, and they are what you really want, and they'd be quite different from HC(O)R formyl anyway. If I look for the bonds/dihedrals and then don't find them, what's the next step? Search the literature to see if anyone else has used this functional group, but probably give up and use acetyl, like everybody else does. You have to have a compelling reason to want to bother to parameterize this group, and I'd suggest you get a lot more experience first. Mark -- 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] Gromacs installation
On 30/07/2012 6:56 PM, rama david wrote: Hi GROMACS FRIENDS, I have dell T3500 precision, 64 bits, 6C workstation with fedora operating system. I want to install gromacs in parallel mode with mpi... I am planning to performed Replica Exchange Molecular Dynamics ( REMD ). As per REMD instruction http://www.gromacs.org/Documentation/How-tos/REMD?highlight=remd, GROMACS should not compile in threading. I install open mpi with command line yum -y install openmpi. I found that fedora add/remove software package has gromacs 4.5.5 version that can be easily installed by command yum .. It enlisted with total 15 different packages : eg.. two packages.. 1. GROMACS Open MPI binaries and libraries 2 . GROMACS OPEN MPI shared libraries and a more.. Please can you tell me which packages I have to install so that I can run GROMACS 4.5.5 in parallel to do REMD. None of those are officially supported by the GROMACS team, so you're on your own to consult the metadata about each package (and maybe its dependencies) and see which one you want to use. Or do a source build per the instructions on the GROMACS web page. Mark -- 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] Diagnosing + system blowing up
In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of formyl group ( as you see earlier) . If I don't use these, so what atom types?! I sent an email to Prof.Roux the author of this article http://www.pnas.org/content/101/1/117.abstract . He suggested me to use the parameters of formamide the charmm36.rtf file . RESI FORM 0.00 ! CH3NO formamide, adm jr. GROUP ATOM HA HGR52 0.08 ! ATOM C CG2O1 0.42 ! O Hc ATOM N NG2S2 -0.69 ! \\ / ATOM HC HGP1 0.35 ! C--N ATOM HT HGP1 0.35 ! / \ ATOM O OG2D1 -0.51 ! HA Ht I found something similar to what I used here for my defined formyl group.Would this be useful? Sincerely, Shima - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Monday, July 30, 2012 1:22 PM Subject: Re: [gmx-users] Diagnosing + system blowing up On 30/07/2012 6:36 PM, Shima Arasteh wrote: > Thanks dear Mark. > Actually the atomtype C is more suitable for C atom of formyl and not CT1! > > The same as before I get the no default bonds/angles/dihedral errors . You > explained what I am suppose. > I can understand the way of matching the coordinate file and atom types in > .rtp file. But it's not clear for me that what I am supposed to check? bonds? > I don't know what I need to do. Your .rtp entry has to specify atom types. Those atom types have to make chemical sense. Then there have to be bond/angle/dihedral parameters for all the combinations you want to use. It may be that this is impossible (and pdb2gmx is having trouble, which suggests this is true), but you can't know without looking at the force field files. This is about the third time I've said to go looking for formyl atom types in atomtypes.atp. They're probably not there. Atom types for HC(O)N(H)R... are almost certainly not there, and they are what you really want, and they'd be quite different from HC(O)R formyl anyway. > If I look for the bonds/dihedrals and then don't find them, what's the next > step? Search the literature to see if anyone else has used this functional group, but probably give up and use acetyl, like everybody else does. You have to have a compelling reason to want to bother to parameterize this group, and I'd suggest you get a lot more experience first. Mark -- gmx-users mailing list gmx-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] Gromacs installation
If you install package 1 on your list, the second one will be installed as well (ie you need both of them). // Linus On Mon, Jul 30, 2012 at 10:56 AM, rama david wrote: > Hi GROMACS FRIENDS, > I have dell T3500 precision, 64 bits, 6C workstation with fedora > operating system. > I want to install gromacs in parallel mode with mpi... > I am planning to performed Replica Exchange Molecular Dynamics ( REMD ). > As per REMD instruction > http://www.gromacs.org/Documentation/How-tos/REMD?highlight=remd, > GROMACS should not compile in threading. > I install open mpi with command line yum -y install openmpi. > I found that fedora add/remove software package has gromacs 4.5.5 > version that can be > easily installed by command yum .. > It enlisted with total 15 different packages : eg.. two packages.. > > 1. GROMACS Open MPI binaries and libraries > 2 . GROMACS OPEN MPI shared libraries > > and a more.. > > Please can you tell me which packages I have to install so that I can > run GROMACS 4.5.5 in parallel to do REMD. > > > Thank you in advance > Have a nice day.. > > > With Best Wishes and regards. > Rama David > -- > 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
[gmx-users] Gromacs installation
Hi GROMACS FRIENDS, I have dell T3500 precision, 64 bits, 6C workstation with fedora operating system. I want to install gromacs in parallel mode with mpi... I am planning to performed Replica Exchange Molecular Dynamics ( REMD ). As per REMD instruction http://www.gromacs.org/Documentation/How-tos/REMD?highlight=remd, GROMACS should not compile in threading. I install open mpi with command line yum -y install openmpi. I found that fedora add/remove software package has gromacs 4.5.5 version that can be easily installed by command yum .. It enlisted with total 15 different packages : eg.. two packages.. 1. GROMACS Open MPI binaries and libraries 2 . GROMACS OPEN MPI shared libraries and a more.. Please can you tell me which packages I have to install so that I can run GROMACS 4.5.5 in parallel to do REMD. Thank you in advance Have a nice day.. With Best Wishes and regards. Rama David -- 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] Diagnosing + system blowing up
On 30/07/2012 6:36 PM, Shima Arasteh wrote: Thanks dear Mark. Actually the atomtype C is more suitable for C atom of formyl and not CT1! The same as before I get the no default bonds/angles/dihedral errors . You explained what I am suppose. I can understand the way of matching the coordinate file and atom types in .rtp file. But it's not clear for me that what I am supposed to check? bonds? I don't know what I need to do. Your .rtp entry has to specify atom types. Those atom types have to make chemical sense. Then there have to be bond/angle/dihedral parameters for all the combinations you want to use. It may be that this is impossible (and pdb2gmx is having trouble, which suggests this is true), but you can't know without looking at the force field files. This is about the third time I've said to go looking for formyl atom types in atomtypes.atp. They're probably not there. Atom types for HC(O)N(H)R... are almost certainly not there, and they are what you really want, and they'd be quite different from HC(O)R formyl anyway. If I look for the bonds/dihedrals and then don't find them, what's the next step? Search the literature to see if anyone else has used this functional group, but probably give up and use acetyl, like everybody else does. You have to have a compelling reason to want to bother to parameterize this group, and I'd suggest you get a lot more experience first. Mark -- 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] Diagnosing + system blowing up
Thanks dear Mark. Actually the atomtype C is more suitable for C atom of formyl and not CT1! The same as before I get the no default bonds/angles/dihedral errors . You explained what I am suppose. I can understand the way of matching the coordinate file and atom types in .rtp file. But it's not clear for me that what I am supposed to check? bonds? I don't know what I need to do. If I look for the bonds/dihedrals and then don't find them, what's the next step? Sincerely, Shima - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Monday, July 30, 2012 6:29 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 29/07/2012 11:40 PM, Shima Arasteh wrote: > I did the exercise as you said. > A .pdb file of ACE and VAL. I ran the pdb2gmx, entered none as the N-terminus > and COO- as the C-terminus. The atomtyps that charmm selects for the acetyl > is as below: > 1 CT3 1 ACE CH3 1 -0.27 12.011 ; qtot >-0.27 > 2 HA 1 ACE HH31 2 0.09 1.008 ; qtot >-0.18 > 3 HA 1 ACE HH32 3 0.09 1.008 ; qtot >-0.09 > 4 HA 1 ACE HH33 4 0.09 1.008 ; qtot >0 > 5 C 1 ACE C 5 0.51 12.011 ; qtot >0.51 > 6 O 1 ACE O 6 -0.51 15.999 ; qtot >0 > I thought that when H is instead of CH3 group, I will have a C atom of type > CT1 in formyl. Look at the definition of CT1 in atomtypes.atp... does the description there suit HC(O)NH-? > > But when I entered the grompp command I got 13 errors as kind of the errors > got befor ( no default bonds or... ) > > What do you suggest me? Any other homework to do? I will do! I already talked about looking to see whether formyl atom types even exist... pdb2gmx has to match the atom names in the coordinate file to the atom names in the .rtp to look up the atom types and then there has to be a bonded type that matches those types. These errors occur when the latter is impossible. So you need to find out if these types exist in your force field. Mark > > Sincerely, > Shima > > > - Original Message - > From: Shima Arasteh > To: Discussion list for GROMACS users > Cc: > Sent: Sunday, July 29, 2012 2:44 PM > Subject: Re: [gmx-users] Diagnosing + system blowing up > > > > Uh-huh.. :-) ;-) > I visualized the .pdb in VMD and it seems OK. > > All right, I will do the exercise for tonight. :-) > > Thanks Mark. > > > Sincerely, > Shima > > > - Original Message - > From: Mark Abraham > To: Discussion list for GROMACS users > Cc: > Sent: Sunday, July 29, 2012 6:54 AM > Subject: Re: [gmx-users] Diagnosing + system blowing up > > On 29/07/2012 4:47 AM, Shima Arasteh wrote: >> >> Dear Mark, Thanks for your suggestions. >> Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is >> tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all! > Uh-huh... there's a known initial issue with a bond between 18 and 1 and > later issues with 1-4 interaction between 5 and 1... and now you think > there is a bond from 18 to 5? This makes no sense. > >> However I see this pair in the [pairs] section of topology ! >> So I can get the result of an inappropriate bond interaction here! Correct? >> Now I think it's not necessary to go through the diagnosing steps any more! >> :-( >> What is my duty right now?! >> >> Is this problem supposed to be fixed in the .pdb file? What's wrong with the >> pdb file? What about erasing the unexpected bond interactions in topology >> file? > As I've said, at least one of your topology and initial coordinates > don't make sense. If you visualize the coordinates and they make sense, > then you need to go back and get a proper topology, like Justin said. > Blindly erasing interactions is ineffective. Go and design it properly, > probably from the beginning or from what Justin said. As an exercise, > get a simulation of Val with acetyl and some C-terminal capping residues > working. Then work out from that example how to define and use an .rtp > entry that is acetyl-Val. Then adapt that to formyl-Val. > > Mark > >> >> >> Sincerely, >> Shima >> >> >> - Original Message - >> From: Mark Abraham >> To: Discussion list for GROMACS users >> Cc: >> Sent: Saturday, July 28, 2012 7:15 PM >> Subject: Re: [gmx-users] Diagnoding + system blowing up >> >> On 28/07/2012 9:34 PM, Shima Arasteh wrote: >>> Hi all, >>> >>> My system has got BLOWING UP . I followed the protocol in >>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as >>> below: >>> >>> Step 1: If the crash is happening relatively early (within a few steps), >>> set nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the >>> resulting trajectory to see which atoms/residues/molecules become unstabl
[gmx-users] RE: Re: Help of mdrun-gpu (Mark Abraham)
Dear Mark, Thank you for your reply. I have read the documentations from http://www.gromacs.org/Documentation/Installation_Instructions/GPUs and also, from gromacs manual. I configured my system strictly followed by the instruction from it. My GPU is GTX-480, which is supported by gromacs. Then, How should I figure out the problem? Jiangfeng. On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote: > Dear All, > > I just configured the mdrun-gpu. When I tested "mdrun-gpu" by running > gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it > failed with segmentation fault. I don't think the system has any equilibrium > problem since it works fine in "mdrun". I will appreciate a lot if anyone > could help me for it. > > Best Wishes, > > Jiangfeng. > Have you read the available documentation? Do you have a supported GPU? Mark -- 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] RE: gmx-users Digest, Vol 99, Issue 113
Dear Mark, Thank you for your reply. I have read the documentations from http://www.gromacs.org/Documentation/Installation_Instructions/GPUs and also, from gromacs manual. I configured my system strictly followed by the instruction from it. My GPU is GTX-480, which is supported by gromacs. Then, How should I figure out the problem? Jiangfeng. On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote: > Dear All, > > I just configured the mdrun-gpu. When I tested "mdrun-gpu" by running > gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it > failed with segmentation fault. I don't think the system has any equilibrium > problem since it works fine in "mdrun". I will appreciate a lot if anyone > could help me for it. > > Best Wishes, > > Jiangfeng. > Have you read the available documentation? Do you have a supported GPU? Mark -- 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
