<font><font face="trebuchet ms,sans-serif"><div><br></div><div>First i had simulation of the protein alone in united atom gromacs force field by -ff gmx in pdb2gmx</div><div>now i am unable to run the protein-ligand complex for the same protein with a ligand,</div>
<div> it says the following error due to itp file generated from PRODRG, </div><div>if i change the force field its says atom mismatch............. Please help me....</div><div><br></div><div>What is the way to run the simulation</div>
<div><br></div><div>grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr</div><div> :-) G R O M A C S (-:</div><div><br></div><div> GRoups of Organic Molecules in ACtion for Science</div>
<div><br></div><div> :-) VERSION 4.0.7 (-:</div><div><br></div><div><br></div><div> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.</div><div> Copyright (c) 1991-2000, University of Groningen, The Netherlands.</div>
<div> Copyright (c) 2001-2008, The GROMACS development team,</div><div> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.</div><div><br></div><div> This program is free software; you can redistribute it and/or</div>
<div> modify it under the terms of the GNU General Public License</div><div> as published by the Free Software Foundation; either version 2</div><div> of the License, or (at your option) any later version.</div>
<div><br></div><div> :-) grompp-4.0.7 (-:</div><div><br></div><div>Option Filename Type Description</div><div>------------------------------------------------------------</div><div>
-f em.mdp Input, Opt! grompp input file with MD parameters</div><div> -po mdout.mdp Output grompp input file with MD parameters</div><div> -c prt_b4ion.pdb Input Structure file: gro g96 pdb tpr tpb tpa</div>
<div> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa</div><div> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa</div><div> -n index.ndx Input, Opt. Index file</div>
<div> -p prt.top Input Topology file</div><div> -pp processed.top Output, Opt. Topology file</div><div> -o prt_b4ion.tpr Output Run input file: tpr tpb tpa</div><div> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt</div>
<div> -e ener.edr Input, Opt. Energy file: edr ene</div><div><br></div><div>Option Type Value Description</div><div>------------------------------------------------------</div><div>-[no]h bool no Print help info and quit</div>
<div>-nice int 0 Set the nicelevel</div><div>-[no]v bool yes Be loud and noisy</div><div>-time real -1 Take frame at or first after this time.</div><div>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual</div>
<div> sites</div><div>-maxwarn int 0 Number of allowed warnings during input processing</div><div>-[no]zero bool no Set parameters for bonded interactions without</div><div>
defaults to zero instead of generating an error</div><div>-[no]renum bool yes Renumber atomtypes and minimize number of</div><div> atomtypes</div><div><br></div>
<div>Ignoring obsolete mdp entry 'title'</div><div>Ignoring obsolete mdp entry 'cpp'</div><div><br></div><div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#</div><div>checking input for internal consistency...</div>
<div>processing topology...</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp</div>
<div>Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp</div><div>Generated 1284 of the 1485 non-bonded parameter combinations</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp</div>
<div>Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp</div><div><br></div><div>-------------------------------------------------------</div><div>Program grompp-4.0.7, VERSION 4.0.7</div><div>Source code file: toppush.c, line: 947</div>
<div><br></div><div>Fatal error:</div><div>Atomtype CR1 not found</div><div>-------------------------------------------------------</div><div><br></div><div>"I Caught It In the Face" (P.J. Harvey)</div><div><br>
</div><div>[</div><div><br></div><div> grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr</div><div> :-) G R O M A C S (-:</div><div><br></div><div> GROtesk MACabre and Sinister</div>
<div><br></div><div> :-) VERSION 4.0.7 (-:</div><div><br></div><div><br></div><div> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.</div><div> Copyright (c) 1991-2000, University of Groningen, The Netherlands.</div>
<div> Copyright (c) 2001-2008, The GROMACS development team,</div><div> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.</div><div><br></div><div> This program is free software; you can redistribute it and/or</div>
<div> modify it under the terms of the GNU General Public License</div><div> as published by the Free Software Foundation; either version 2</div><div> of the License, or (at your option) any later version.</div>
<div><br></div><div> :-) grompp-4.0.7 (-:</div><div><br></div><div>Option Filename Type Description</div><div>------------------------------------------------------------</div><div>
-f em.mdp Input, Opt! grompp input file with MD parameters</div><div> -po mdout.mdp Output grompp input file with MD parameters</div><div> -c prt_b4ion.pdb Input Structure file: gro g96 pdb tpr tpb tpa</div>
<div> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa</div><div> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa</div><div> -n index.ndx Input, Opt. Index file</div>
<div> -p prt.top Input Topology file</div><div> -pp processed.top Output, Opt. Topology file</div><div> -o prt_b4ion.tpr Output Run input file: tpr tpb tpa</div><div> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt</div>
<div> -e ener.edr Input, Opt. Energy file: edr ene</div><div><br></div><div>Option Type Value Description</div><div>------------------------------------------------------</div><div>-[no]h bool no Print help info and quit</div>
<div>-nice int 0 Set the nicelevel</div><div>-[no]v bool yes Be loud and noisy</div><div>-time real -1 Take frame at or first after this time.</div><div>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual</div>
<div> sites</div><div>-maxwarn int 0 Number of allowed warnings during input processing</div><div>-[no]zero bool no Set parameters for bonded interactions without</div><div>
defaults to zero instead of generating an error</div><div>-[no]renum bool yes Renumber atomtypes and minimize number of</div><div> atomtypes</div><div><br></div>
<div>Ignoring obsolete mdp entry 'title'</div><div>Ignoring obsolete mdp entry 'cpp'</div><div><br></div><div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#</div><div>checking input for internal consistency...</div>
<div>processing topology...</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp</div>
<div>Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp</div><div>Generated 1284 of the 1485 non-bonded parameter combinations</div><div>Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp</div>
<div>Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp</div><div>Excluding 3 bonded neighbours molecule type 'Protein_A'</div><div>Excluding 3 bonded neighbours molecule type 'DRG'</div><div>
Excluding 2 bonded neighbours molecule type 'SOL'</div><div><br></div><div>NOTE 1 [file prt.top, line 18947]:</div><div> System has non-zero total charge: -9.999978e-01</div><div> </div><div><br></div><div><br>
</div>
<div>processing coordinates...</div><div><br></div><div>-------------------------------------------------------</div><div>Program grompp-4.0.7, VERSION 4.0.7</div><div>Source code file: grompp.c, line: 362</div><div><br>
</div>
<div>Fatal error:</div><div>number of coordinates in coordinate file (prt_b4ion.pdb, 79463)</div><div> does not match topology (prt.top, 79455)</div><div>-------------------------------------------------------</div>
<div><br></div><div>"Sometimes Life is Obscene" (Black Crowes)</div><div><br></div></font></font><div><br></div>-- <br><div><font face="comic sans ms,sans-serif"></font>-- <br><div><br><font face="comic sans ms,sans-serif"></font></div>
<div style="font-family:verdana,sans-serif"><b><font>Yours Sincerely,</font></b></div><div style="font-family:verdana,sans-serif"><b><font>B. Sarath Kumar, M.S (By Research),<br>Tissue Culture and Drug Discovery Lab,<br>
Centre for Biotechnology,<br>
Anna University, Chennai.</font></b></div></div><br>