On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran < [email protected]> 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 Input Structure 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 > -p prt.top Input Topology 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 > -nice int 0 Set the nicelevel > -[no]v bool yes Be loud and noisy > -time real -1 Take frame at or first after this time. > -[no]rmvsbds bool yes Remove constant bonded interactions with > virtual > sites > -maxwarn int 0 Number of allowed warnings during input > processing > -[no]zero bool 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 > ------------------------------------------------------------ > -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 Input Structure 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 > -p prt.top Input Topology 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 > -nice int 0 Set the nicelevel > -[no]v bool yes Be loud and noisy > -time real -1 Take frame at or first after this time. > -[no]rmvsbds bool yes Remove constant bonded interactions with > virtual > sites > -maxwarn int 0 Number of allowed warnings during input > processing > -[no]zero bool 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.5# > 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 > Excluding 3 bonded neighbours molecule type 'Protein_A' > Excluding 3 bonded neighbours molecule type 'DRG' > Excluding 2 bonded neighbours molecule type 'SOL' > > NOTE 1 [file prt.top, line 18947]: > System has non-zero total charge: -9.999978e-01 > > > > processing coordinates... > > ------------------------------------------------------- > Program grompp-4.0.7, VERSION 4.0.7 > Source code file: grompp.c, line: 362 > > Fatal error: > number of coordinates in coordinate file (prt_b4ion.pdb, 79463) > does not match topology (prt.top, 79455) > ------------------------------------------------------- > > "Sometimes Life is Obscene" (Black Crowes) > > > -- > -- > > *Yours Sincerely,* > *B. Sarath Kumar, M.S (By Research), > Tissue Culture and Drug Discovery Lab, > Centre for Biotechnology, > Anna University, Chennai.* > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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