Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
A lot of thanks to your "charitable mood" now the things has been resolved :) . Thanks again. On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks again >> > > For the record, I didn't ask that you send me your files so I could > troubleshoot for you. Luckily for you I'm in a charitable mood this > morning, so I took a look ;) > > Your problem is that you have a [molecules] directive in oct.itp. Please > refer to the documentation for the difference between a .top topology and a > .itp topology: > > http://www.gromacs.org/Documentation/File_Formats/.itp_File > > The presence of this [molecules] directive tells grompp that the first thing > it should expect is a block of octanol, when in fact your coordinate file > has the protein first (starting with Ser-Leu, as I suspected). You then > have "1-octanol 1" in your topol.top, which says you're including another > random octanol molecule somewhere later. > > You need a single [molecules] directive in the .top, which must match the > order of the coordinate file. Once you've got that, things should work > fine. > > -Justin > > >>> From the error It seems that I have placed the octane molecule before >> >> the protein but it is not the case, I dont know why grompp is reading >> parameters for octane first and expecting it to match with protein. I >> know that its my problem and I have to think about >> that but just for the reference for you I am attaching the coordinate >> and topology files. >> >> On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul wrote: >>> >>> >>> bipin singh wrote: Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error. >>> Looking closer at the error, what's happening is your octanol molecule is >>> in >>> a place where the topology expects the amino acid sequence Ser-Leu. >>> Perhaps >>> that will help you track down the source of the problem. It seems to me >>> that your octanol molecule occurs earlier in the coordinate file than it >>> does in the topology. >>> >>> If you still can't locate the problem, then you can always start over >>> building your system in a known order, checking the alignment of the >>> coordinate file and topology at every step. >>> >>> -Justin >>> >>> On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul wrote: > > > Biswajit Gorai wrote: >> >> Dear Bipin, >> Edit your topology file as: >> >> ### >> ; Include forcefield parameters >> #include "amber99sb-ildn.ff/forcefield.itp" >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #include "topol_Ion_chain_A2.itp" >> >> *#include "oct.itp"* >> > If oct.itp introduces new atom types (as the original .top does, for > GAFF), > placing this topology here will result in a fatal error since there is > a > new > [atomtypes] directive that is introduced after the protein > [moleculetype]. > If oct.itp does not introduce any new atom types, its location within > the > system topology is irrelevant. > >> ; Include water topology >> #include "amber99sb-ildn.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "amber99sb-ildn.ff/ions.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> Ion_chain_A2 1 >> *1-octanol 1 >> * >> *SOL 8987* > > > Depending on the order of the coordinate file, it may not be possible > to > merge the SOL entries in this way. > > -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 >>> -- >>> ==
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
bipin singh wrote: Thanks again For the record, I didn't ask that you send me your files so I could troubleshoot for you. Luckily for you I'm in a charitable mood this morning, so I took a look ;) Your problem is that you have a [molecules] directive in oct.itp. Please refer to the documentation for the difference between a .top topology and a .itp topology: http://www.gromacs.org/Documentation/File_Formats/.itp_File The presence of this [molecules] directive tells grompp that the first thing it should expect is a block of octanol, when in fact your coordinate file has the protein first (starting with Ser-Leu, as I suspected). You then have "1-octanol 1" in your topol.top, which says you're including another random octanol molecule somewhere later. You need a single [molecules] directive in the .top, which must match the order of the coordinate file. Once you've got that, things should work fine. -Justin From the error It seems that I have placed the octane molecule before the protein but it is not the case, I dont know why grompp is reading parameters for octane first and expecting it to match with protein. I know that its my problem and I have to think about that but just for the reference for you I am attaching the coordinate and topology files. On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error. Looking closer at the error, what's happening is your octanol molecule is in a place where the topology expects the amino acid sequence Ser-Leu. Perhaps that will help you track down the source of the problem. It seems to me that your octanol molecule occurs earlier in the coordinate file than it does in the topology. If you still can't locate the problem, then you can always start over building your system in a known order, checking the alignment of the coordinate file and topology at every step. -Justin On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul wrote: Biswajit Gorai wrote: Dear Bipin, Edit your topology file as: ### ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" *#include "oct.itp"* If oct.itp introduces new atom types (as the original .top does, for GAFF), placing this topology here will result in a fatal error since there is a new [atomtypes] directive that is introduced after the protein [moleculetype]. If oct.itp does not introduce any new atom types, its location within the system topology is irrelevant. ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 *1-octanol 1 * *SOL 8987* Depending on the order of the coordinate file, it may not be possible to merge the SOL entries in this way. -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 -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (5
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
bipin singh wrote: Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error. Looking closer at the error, what's happening is your octanol molecule is in a place where the topology expects the amino acid sequence Ser-Leu. Perhaps that will help you track down the source of the problem. It seems to me that your octanol molecule occurs earlier in the coordinate file than it does in the topology. If you still can't locate the problem, then you can always start over building your system in a known order, checking the alignment of the coordinate file and topology at every step. -Justin On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul wrote: Biswajit Gorai wrote: Dear Bipin, Edit your topology file as: ### ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" *#include "oct.itp"* If oct.itp introduces new atom types (as the original .top does, for GAFF), placing this topology here will result in a fatal error since there is a new [atomtypes] directive that is introduced after the protein [moleculetype]. If oct.itp does not introduce any new atom types, its location within the system topology is irrelevant. ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 *1-octanol 1 * *SOL 8987* Depending on the order of the coordinate file, it may not be possible to merge the SOL entries in this way. -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 -- 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] Re: How to add dihedral information from the GAFF topology
Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error. On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul wrote: > > > Biswajit Gorai wrote: >> >> Dear Bipin, >> Edit your topology file as: >> >> ### >> ; Include forcefield parameters >> #include "amber99sb-ildn.ff/forcefield.itp" >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #include "topol_Ion_chain_A2.itp" >> >> *#include "oct.itp"* >> > > If oct.itp introduces new atom types (as the original .top does, for GAFF), > placing this topology here will result in a fatal error since there is a new > [atomtypes] directive that is introduced after the protein [moleculetype]. > If oct.itp does not introduce any new atom types, its location within the > system topology is irrelevant. > >> ; Include water topology >> #include "amber99sb-ildn.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "amber99sb-ildn.ff/ions.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> Ion_chain_A2 1 >> *1-octanol 1 >> * >> *SOL 8987* > > > Depending on the order of the coordinate file, it may not be possible to > merge the SOL entries in this way. > > -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 -- --- Regards, Bipin Singh -- 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] Re: How to add dihedral information from the GAFF topology
Biswajit Gorai wrote: Dear Bipin, Edit your topology file as: ### ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" *#include "oct.itp"* If oct.itp introduces new atom types (as the original .top does, for GAFF), placing this topology here will result in a fatal error since there is a new [atomtypes] directive that is introduced after the protein [moleculetype]. If oct.itp does not introduce any new atom types, its location within the system topology is irrelevant. ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 *1-octanol 1 * *SOL 8987* Depending on the order of the coordinate file, it may not be possible to merge the SOL entries in this way. -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] Re: How to add dihedral information from the GAFF topology
Dear Bipin, Edit your topology file as: ### ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" *#include "oct.itp"* ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 *1-octanol 1 * *SOL 8987* ### It may be helpful to you. Biswajit -- 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] Re: How to add dihedral information from the GAFF topology
bipin singh wrote: Thanks for your suggestions. Now I am getting the following error during grompp Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not match (C1 - N) Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not match (C2 - CA) Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not match (H4 - HA) Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not match (H5 - CB) Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not match (C3 - HB1) Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not match (H6 - HB2) Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not match (H7 - OG) Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not match (C4 - HG) Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not match (H8 - C) Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not match (H9 - O) Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not match (C5 - N) Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not match (H10 - H) Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not match (H11 - CA) Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not match (C6 - HA) Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not match (H12 - CB) Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not match (H13 - HB1) Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not match (C7 - HB2) Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not match (H14 - CG) Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not match (H15 - HG) Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not match (C8 - CD1) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 55]: 28782 non-matching atom names atom names from topol.top will be used atom names from box_prot_oct_sol.gro will be ignored The order of atoms in coordinate file and order of [molecules] directive are same. If that were true, you wouldn't be getting this error. Check your files very carefully. Something doesn't line up. -Justin I have checked on the gromacs forum and also the documentation but not able to rectify the problem. This is how I included the octane topology in .top file # ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "oct.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 SOL 565 1-octanol 1 SOL 8422 Please provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your inputs. I have followed your suggestion and included the .itp for the octane molecule (containing atomtype definition for new atoms) in the topology file(.top) of the whole system (prot+oct+water). but during grompp it produce error and results in termination due to non matching numbers (27 atoms of octane molecule) between coordinate file and topology file. WARNING 1 [file 111-87-5.top, line 15]: Overriding atomtype h1 WARNING 2 [file 111-87-5.top, line 17]: Overriding atomtype c3 WARNING 3 [file 111-87-5.top, line 19]: Overriding atomtype ho It appears that you have somehow duplicated atom types and they are overriding each other. Generated 4656 of the 4656 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 4656 of the 4656 1-4 parameter combinations Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 55]: System has non-zero total charge: -9.89e-01 Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (box_oct_sol.gro, 54297) does not match topology (topol.top, 54324) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Did you follow the link? Surely you would have found: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_matc
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your suggestions. Now I am getting the following error during grompp Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not match (C1 - N) Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not match (C2 - CA) Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not match (H4 - HA) Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not match (H5 - CB) Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not match (C3 - HB1) Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not match (H6 - HB2) Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not match (H7 - OG) Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not match (C4 - HG) Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not match (H8 - C) Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not match (H9 - O) Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not match (C5 - N) Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not match (H10 - H) Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not match (H11 - CA) Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not match (C6 - HA) Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not match (H12 - CB) Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not match (H13 - HB1) Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not match (C7 - HB2) Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not match (H14 - CG) Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not match (H15 - HG) Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not match (C8 - CD1) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 55]: 28782 non-matching atom names atom names from topol.top will be used atom names from box_prot_oct_sol.gro will be ignored The order of atoms in coordinate file and order of [molecules] directive are same. I have checked on the gromacs forum and also the documentation but not able to rectify the problem. This is how I included the octane topology in .top file # ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "oct.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 SOL 565 1-octanol 1 SOL 8422 Please provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your inputs. >> I have followed your suggestion and included the .itp for the octane >> molecule (containing atomtype definition for new atoms) in the >> topology file(.top) of the whole system (prot+oct+water). but during >> grompp it produce error and results in termination due to non matching >> numbers (27 atoms of octane molecule) between coordinate file and >> topology file. >> >> >> >> WARNING 1 [file 111-87-5.top, line 15]: >> Overriding atomtype h1 >> >> >> WARNING 2 [file 111-87-5.top, line 17]: >> Overriding atomtype c3 >> >> >> WARNING 3 [file 111-87-5.top, line 19]: >> Overriding atomtype ho >> > > It appears that you have somehow duplicated atom types and they are > overriding each other. > > >> Generated 4656 of the 4656 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 0.5 >> Generated 4656 of the 4656 1-4 parameter combinations >> Excluding 3 bonded neighbours molecule type '1-octanol' >> Excluding 3 bonded neighbours molecule type 'Protein_chain_A' >> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' >> Excluding 3 bonded neighbours molecule type '1-octanol' >> Excluding 2 bonded neighbours molecule type 'SOL' >> Excluding 2 bonded neighbours molecule type 'SOL' >> >> NOTE 1 [file topol.top, line 55]: >> System has non-zero total charge: -9.89e-01 >> >> Program grompp, VERSION 4.5.3 >> Source code file: grompp.c, line: 523 >> >> Fatal error: >> number of coordinates in coordinate file (box_oct_sol.gro, 54297) >> does not match topology (topol.top, 54324) >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> > > Did you follow the link? Surely you would have found: > > http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology > >
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
bipin singh wrote: Thanks for your inputs. I have followed your suggestion and included the .itp for the octane molecule (containing atomtype definition for new atoms) in the topology file(.top) of the whole system (prot+oct+water). but during grompp it produce error and results in termination due to non matching numbers (27 atoms of octane molecule) between coordinate file and topology file. WARNING 1 [file 111-87-5.top, line 15]: Overriding atomtype h1 WARNING 2 [file 111-87-5.top, line 17]: Overriding atomtype c3 WARNING 3 [file 111-87-5.top, line 19]: Overriding atomtype ho It appears that you have somehow duplicated atom types and they are overriding each other. Generated 4656 of the 4656 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 4656 of the 4656 1-4 parameter combinations Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 55]: System has non-zero total charge: -9.89e-01 Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (box_oct_sol.gro, 54297) does not match topology (topol.top, 54324) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Did you follow the link? Surely you would have found: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin ##3 this is how I included the itp for the octane molecule in .top file ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "octane.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 1-octanol 1 SOL 565 SOL 8495 # --- Please provide your comments. On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other information. I followed your suggestions and able to generate a biphasic system of water/octane containing a protein molecule. But, when I tried grompp on this biphasic system (containing octane+water+protein), it results in error even if I include the topologies in forcefield.itp file. The error was Fatal error: Atomtype hc not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors If you introduce a new atomtype in your topology somewhere (presumably in one of the GAFF topologies), then you have to declare them in an [atomtypes] directive in the appropriate place in the .top file. These types are case sensitive as well. For dealing with GAFF-type topologies, assuming you can #include them within whatever AMBER force field you've chosen (up to you to prove), you can do something like: #include "amberXX.ff/forcefield.itp" #include "ligand.itp" [ moleculetype ] ;name nrexcl Protein 3 (etc) The inclusion of the ligand topology (at this specific location) will add the new [atomtypes] at the appropriate level of precedence, before any [moleculetypes] are declared. -Justin On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As David said, the topologies stand on their own. You do not need to call any further information from anywhere. The .top that you downloaded begins with a [defaults] directive, declares atom types, and proceeds through the rest of the topology with explicit parameters. As you said these topologies are self supporting and we do not need to change
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your inputs. I have followed your suggestion and included the .itp for the octane molecule (containing atomtype definition for new atoms) in the topology file(.top) of the whole system (prot+oct+water). but during grompp it produce error and results in termination due to non matching numbers (27 atoms of octane molecule) between coordinate file and topology file. WARNING 1 [file 111-87-5.top, line 15]: Overriding atomtype h1 WARNING 2 [file 111-87-5.top, line 17]: Overriding atomtype c3 WARNING 3 [file 111-87-5.top, line 19]: Overriding atomtype ho Generated 4656 of the 4656 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 4656 of the 4656 1-4 parameter combinations Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 55]: System has non-zero total charge: -9.89e-01 Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (box_oct_sol.gro, 54297) does not match topology (topol.top, 54324) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ##3 this is how I included the itp for the octane molecule in .top file ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "octane.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 1-octanol 1 SOL 565 SOL 8495 # --- Please provide your comments. On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply. >> >> Yes, you are right that these topologies are self supporting and there >> is no need to to call any other information. I followed your >> suggestions and able to generate a biphasic system of water/octane >> containing a protein molecule. But, when I tried grompp on this >> biphasic system (containing octane+water+protein), it results in error >> even if I include the topologies in forcefield.itp file. >> >> The error was >> >> Fatal error: >> Atomtype hc not found >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> > > If you introduce a new atomtype in your topology somewhere (presumably in > one of the GAFF topologies), then you have to declare them in an [atomtypes] > directive in the appropriate place in the .top file. These types are case > sensitive as well. For dealing with GAFF-type topologies, assuming you can > #include them within whatever AMBER force field you've chosen (up to you to > prove), you can do something like: > > #include "amberXX.ff/forcefield.itp" > > #include "ligand.itp" > > [ moleculetype ] > ;name nrexcl > Protein 3 > > (etc) > > The inclusion of the ligand topology (at this specific location) will add > the new [atomtypes] at the appropriate level of precedence, before any > [moleculetypes] are declared. > > > -Justin > >> On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul wrote: >>> >>> >>> bipin singh wrote: Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. >>> As David said, the topologies stand on their own. You do not need to >>> call >>> any further information from anywhere. The .top that you downloaded >>> begins >>> with a [defaults] directive, declares atom types, and proceeds through >>> the >>> rest of the topology with explicit parameters. >>> >>> As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedra
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
bipin singh wrote: Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other information. I followed your suggestions and able to generate a biphasic system of water/octane containing a protein molecule. But, when I tried grompp on this biphasic system (containing octane+water+protein), it results in error even if I include the topologies in forcefield.itp file. The error was Fatal error: Atomtype hc not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors If you introduce a new atomtype in your topology somewhere (presumably in one of the GAFF topologies), then you have to declare them in an [atomtypes] directive in the appropriate place in the .top file. These types are case sensitive as well. For dealing with GAFF-type topologies, assuming you can #include them within whatever AMBER force field you've chosen (up to you to prove), you can do something like: #include "amberXX.ff/forcefield.itp" #include "ligand.itp" [ moleculetype ] ;name nrexcl Protein 3 (etc) The inclusion of the ligand topology (at this specific location) will add the new [atomtypes] at the appropriate level of precedence, before any [moleculetypes] are declared. -Justin On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As David said, the topologies stand on their own. You do not need to call any further information from anywhere. The .top that you downloaded begins with a [defaults] directive, declares atom types, and proceeds through the rest of the topology with explicit parameters. As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedral information. ERROR [file oct.top]: No default Proper Dih. types Please provide your suggestions. I certainly don't see how this could have happened. All the dihedral parameters are listed explicitly. The fatal error should have printed a line number in the .top that is problematic, so start by investigating there. If you have modified the topology in any way, then undo the changes and try again. I did not have any trouble using this .top in an unmodified form, so I suspect you've altered it in some way that has broken it. -Justin On Mon, Mar 26, 2012 at 17:29, David van der Spoel wrote: On 2012-03-26 13:55, bipin singh wrote: Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http://virtualchemistry.org/molecules/111-87-5/index.php). I have incorporated all the parameters for atoms, bonds and non-bonded interaction type in the forcefield (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I am not sure how to add the dihedraltypes information in ffbonded.itp from the GAFF topology as to add this information I need the phase and kd for each dihedral. Is this information is available in the GAFF topology provided in the Gromacs database ? This topology is self supporting and you do not need anything else in ffbonded.itp. You should be careful merging such parameters with an existing force field, because strictly speaking these are different force fields. -- 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 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/Suppor
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other information. I followed your suggestions and able to generate a biphasic system of water/octane containing a protein molecule. But, when I tried grompp on this biphasic system (containing octane+water+protein), it results in error even if I include the topologies in forcefield.itp file. The error was Fatal error: Atomtype hc not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply. >> But as far as I understood, in order to use these GAFF topology (for >> e.g. to perform simulation using these topologies) with Gromacs we >> have to incorporate the information from these topologies to the >> existing Amber forcefields in Gromacs or Is there anyway (Possibility >> of using Standalone GAFF parameters in Gromacs) to do it without >> performing this task. >> > > As David said, the topologies stand on their own. You do not need to call > any further information from anywhere. The .top that you downloaded begins > with a [defaults] directive, declares atom types, and proceeds through the > rest of the topology with explicit parameters. > > >> As you said these topologies are self supporting and we do not need to >> change ffbonded.itp, but during grompp I got the following error, may >> be because I have not added the dihedral information. >> >> ERROR [file oct.top]: >> No default Proper Dih. types >> >> Please provide your suggestions. >> > > I certainly don't see how this could have happened. All the dihedral > parameters are listed explicitly. The fatal error should have printed a > line number in the .top that is problematic, so start by investigating > there. If you have modified the topology in any way, then undo the changes > and try again. > > I did not have any trouble using this .top in an unmodified form, so I > suspect you've altered it in some way that has broken it. > > -Justin > > >> >> On Mon, Mar 26, 2012 at 17:29, David van der Spoel >> wrote: >>> >>> On 2012-03-26 13:55, bipin singh wrote: Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http://virtualchemistry.org/molecules/111-87-5/index.php). I have incorporated all the parameters for atoms, bonds and non-bonded interaction type in the forcefield (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I am not sure how to add the dihedraltypes information in ffbonded.itp from the GAFF topology as to add this information I need the phase and kd for each dihedral. Is this information is available in the GAFF topology provided in the Gromacs database ? >>> This topology is self supporting and you do not need anything else in >>> ffbonded.itp. >>> >>> You should be careful merging such parameters with an existing force >>> field, >>> because strictly speaking these are different force fields. >>> >>> -- >>> 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.se http://folding.bmc.uu.se >>> -- >>> 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 >> >> >> >> > > -- > > > 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 -- --- Regards, Bipin Singh -- 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/Maili
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
bipin singh wrote: Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As David said, the topologies stand on their own. You do not need to call any further information from anywhere. The .top that you downloaded begins with a [defaults] directive, declares atom types, and proceeds through the rest of the topology with explicit parameters. As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedral information. ERROR [file oct.top]: No default Proper Dih. types Please provide your suggestions. I certainly don't see how this could have happened. All the dihedral parameters are listed explicitly. The fatal error should have printed a line number in the .top that is problematic, so start by investigating there. If you have modified the topology in any way, then undo the changes and try again. I did not have any trouble using this .top in an unmodified form, so I suspect you've altered it in some way that has broken it. -Justin On Mon, Mar 26, 2012 at 17:29, David van der Spoel wrote: On 2012-03-26 13:55, bipin singh wrote: Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http://virtualchemistry.org/molecules/111-87-5/index.php). I have incorporated all the parameters for atoms, bonds and non-bonded interaction type in the forcefield (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I am not sure how to add the dihedraltypes information in ffbonded.itp from the GAFF topology as to add this information I need the phase and kd for each dihedral. Is this information is available in the GAFF topology provided in the Gromacs database ? This topology is self supporting and you do not need anything else in ffbonded.itp. You should be careful merging such parameters with an existing force field, because strictly speaking these are different force fields. -- 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 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] Re: How to add dihedral information from the GAFF topology
Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedral information. ERROR [file oct.top]: No default Proper Dih. types Please provide your suggestions. On Mon, Mar 26, 2012 at 17:29, David van der Spoel wrote: > On 2012-03-26 13:55, bipin singh wrote: >> >> Hello all, >> >> I am using the GAFF topology provided for octan-1-ol at Gromacs liquid >> database (http://virtualchemistry.org/molecules/111-87-5/index.php). I >> have incorporated all the parameters >> for atoms, bonds and non-bonded interaction type in the forcefield >> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I >> am not sure how to add the dihedraltypes information in ffbonded.itp >> from the GAFF topology as to add this information I need the phase and >> kd for each dihedral. Is this information is available in the GAFF >> topology provided in the Gromacs database ? >> >> > > This topology is self supporting and you do not need anything else in > ffbonded.itp. > > You should be careful merging such parameters with an existing force field, > because strictly speaking these are different force fields. >> >> >> > > > -- > 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.se http://folding.bmc.uu.se > -- > 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 -- --- Regards, Bipin Singh -- 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
