[gmx-users] itp file problem
Hi, For the simulation of a Protein ligand complex, i obtained the itp topology of the ligand from PRODRG 2 server and i ran the simulation of the complex a year back using GROMOS united atom force field by -ff gmx option in GROMACS 3.3 according to the Drg enzyme tutorial now i am unable to run the same protein ligand complex with the recent itp file obtained from the Current PRODRG server for the same ligand, i am getting error ATOM type CR1 not found in GROMACS 4.0.5. I am sure version of gromacs doesnt create any problem. Also i am getting atom mismatch error if i change the ATOM type to CR61, and i completely checked this number of atoms mismatch is only due to the .itp file included in prt.top. Thanks to justin for saying me about the problems in PRODRG topology, and suggesting to do improvements in the topology file for GROMOS force field, But i am totally confused how to edit the itp file. Before i used to include .itp file in .top file and add the residue number as DRG 1. now how to edit the .itp file, Somebody please help me -- -- * **Keep Enjoying !!!* *Yours Sincerely,* *B. Sarath Kumar, M.S (By Research), Tissue Culture and Drug Discovery Lab, Centre for Biotechnology, Anna University, Chennai.* -- 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] itp file problem
On 5/16/12 2:25 PM, Sarath Kumar Baskaran wrote: Hi, For the simulation of a Protein ligand complex, i obtained the itp topology of the ligand from PRODRG 2 server and i ran the simulation of the complex a year back using GROMOS united atom force field by -ff gmx option in GROMACS 3.3 according to the Drg enzyme tutorial now i am unable to run the same protein ligand complex with the recent itp file obtained from the Current PRODRG server for the same ligand, i am getting error ATOM type CR1 not found in GROMACS 4.0.5. I am sure version of gromacs doesnt create any problem. Also i am getting atom mismatch error if i change the ATOM type to CR61, and i completely checked this number of atoms mismatch is only due to the .itp file included in prt.top. Thanks to justin for saying me about the problems in PRODRG topology, and suggesting to do improvements in the topology file for GROMOS force field, But i am totally confused how to edit the itp file. Before i used to include .itp file in .top file and add the residue number as DRG 1. now how to edit the .itp file, Somebody please help me The newer version of the PRODRG server is compatible with Gromos96 43a1, not the old ffgmx, which was a variant of Gromos87. Using 43a1 should solve the problem. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Itp file problem -- Atom type not found
Hi Justin, I had used only Gromos 43 a1 from initially for proteins, but i saw the -ff gmx in the Drug enzyme tutorial, so i tried using this optiion for protein ligand comp[ex simultaitons, also the simulation was able to be performed with -ff gmx for some ligands without the atom type not found error. for all the ligands i used the itp (topology) file from PRODRG only I came accross the problem that u stated with PRODRG in the archives... Now for this protein ligand complex i am unable to used Gromos43a1, it says number of atoms mismatch but that problem of mismatch is due to the itp file included in the .top file For complexes i do add the .itp file in the .top file everytime during simulation... If in case the only way to solve this problem is to make manual improvements in the itp file Can u please help me how to do the adjustmentsI am sorry i dont know how to create a manual itp topology file... Thanks in advance... Sarath Kumar Baskaran -- 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] Itp file problem -- Atom type not found
On 5/9/12 3:13 AM, Sarath Kumar Baskaran wrote: Hi Justin, I had used only Gromos 43 a1 from initially for proteins, but i saw the -ff gmx in the Drug enzyme tutorial, so i tried using this optiion for protein ligand comp[ex simultaitons, also the simulation was able to be performed with -ff gmx for some ligands without the atom type not found error. for all the ligands i used the itp (topology) file from PRODRG only Depending on which version of PRODRG you used, this approach may or may not have been appropriate. I'm assuming the tutorial you followed was John Kerrigan's, which is several years old and relies on an older version of PRODRG. In any case, unmodified PRODRG parameters are insufficiently accurate for simulations, in every case that I have seen. There are better tools available, and greater detail in parameterization is expected. Interpret your results with care, and don't be shocked if reviewers of your papers do not believe the PRODRG results. I came accross the problem that u stated with PRODRG in the archives... Now for this protein ligand complex i am unable to used Gromos43a1, it says number of atoms mismatch but that problem of mismatch is due to the itp file included in the .top file For complexes i do add the .itp file in the .top file everytime during simulation... If in case the only way to solve this problem is to make manual improvements in the itp file Can u please help me how to do the adjustmentsI am sorry i dont know how to create a manual itp topology file... Mismatch between coordinate and topology files is simply due to incorrect counting of molecules or failure to maintain a match between the two. The solution is always the same - take greater care in bookkeeping throughout your workflow. Any time the coordinate file is changed, so too must the topology. Some tools (genbox, genion) do this for you. Anything else is up to you to verify and apply. -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
[gmx-users] itp file problem
First i had simulation of the protein alone in united atom gromacs force field by -ff gmx in pdb2gmx now i am unable to run the protein-ligand complex for the same protein with a ligand, it says the following error due to itp file generated from PRODRG, if i change the force field its says atom mismatch. Please help me What is the way to run the simulation grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp-4.0.7 (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c prt_b4ion.pdb InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -pprt.top InputTopology file -pp processed.top Output, Opt. Topology file -o prt_b4ion.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp Generated 1284 of the 1485 non-bonded parameter combinations Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp --- Program grompp-4.0.7, VERSION 4.0.7 Source code file: toppush.c, line: 947 Fatal error: Atomtype CR1 not found --- I Caught It In the Face (P.J. Harvey) [ grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp-4.0.7 (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c prt_b4ion.pdb InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb
Re: [gmx-users] itp file problem
On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran bskumar.t...@gmail.com wrote: First i had simulation of the protein alone in united atom gromacs force field by -ff gmx in pdb2gmx now i am unable to run the protein-ligand complex for the same protein with a ligand, it says the following error due to itp file generated from PRODRG, if i change the force field its says atom mismatch. Please help me Change the force-field means? Did you change the FF with pdb2gmx, or just in your .top file? What is the way to run the simulation grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp-4.0.7 (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c prt_b4ion.pdb InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -pprt.top InputTopology file -pp processed.top Output, Opt. Topology file -o prt_b4ion.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp Generated 1284 of the 1485 non-bonded parameter combinations Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp --- Program grompp-4.0.7, VERSION 4.0.7 Source code file: toppush.c, line: 947 Fatal error: Atomtype CR1 not found --- I Caught It In the Face (P.J. Harvey) Did you include the ligand's itp file in your .top file? I think you haven't. [ grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp-4.0.7 (-: Option Filename Type Description
Re: [gmx-users] itp file problem
On 5/7/12 7:41 AM, Sarath Kumar Baskaran wrote: First i had simulation of the protein alone in united atom gromacs force field by -ff gmx in pdb2gmx now i am unable to run the protein-ligand complex for the same protein with a ligand, it says the following error due to itp file generated from PRODRG, if i change the force field its says atom mismatch. Please help me PRODRG produces (poor quality) topologies for Gromos96 43A1, not Gromos87 (or ffgmx). One should not use ffgmx for new simulations as it does not perform as well as newer force fields (and other reasons described in the 4.5 manual. Using 43A1 will solve this particular problem, but do note that the PRODRG topology will almost invariably require manual improvements. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin What is the way to run the simulation grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp-4.0.7 (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c prt_b4ion.pdb InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -pprt.top InputTopology file -pp processed.top Output, Opt. Topology file -o prt_b4ion.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp Generated 1284 of the 1485 non-bonded parameter combinations Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp --- Program grompp-4.0.7, VERSION 4.0.7 Source code file: toppush.c, line: 947 Fatal error: Atomtype CR1 not found --- I Caught It In the Face (P.J. Harvey) [ grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2
