<div>Sorry. I will make my statements clear here after.</div>
<div>here is the terminal output after executing grompp -v</div>
<div><br> :-) G R O M A C S (-:</div>
<div> Great Red Oystrich Makes All Chemists Sane</div>
<div> :-) VERSION 4.0.7 (-:</div>
<div><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org/">http://www.gromacs.org</a> for more information.</div>
<div> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.</div>
<div> :-) grompp (-:</div>
<div>Option Filename Type Description<br>------------------------------------------------------------<br> -f grompp.mdp Input, Opt. grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br>
-c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa<br> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-n index.ndx Input, Opt. Index file<br> -p topol.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o topol.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>
-e ener.edr Input, Opt. Energy file: edr ene</div>
<div>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]v bool yes Be loud and noisy<br>
-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>-maxwarn int 0 Number of allowed warnings during input processing<br>
-[no]zero bool no Set parameters for bonded interactions without<br> defaults to zero instead of generating an error<br>-[no]renum bool yes Renumber atomtypes and minimize number of<br>
atomtypes</div>
<div>Ignoring obsolete mdp entry 'title'<br>Ignoring obsolete mdp entry 'cpp'<br>Ignoring obsolete mdp entry 'domain-decomposition'<br>Replacing old mdp entry 'unconstrained-start' by 'continuation'<br>
Ignoring obsolete mdp entry 'dihre-tau'<br>Ignoring obsolete mdp entry 'nstdihreout'<br>Ignoring obsolete mdp entry 'nstcheckpoint'</div>
<div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#</div>
<div>WARNING 1 [file grompp.mdp, line unknown]:<br> Unknown or double left-hand 'bd-temp' in parameter file</div>
<div><br>checking input for internal consistency...</div>
<div>NOTE 1 [file grompp.mdp, line unknown]:<br> The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.</div>
<div>processing topology...<br>Opening library file /usr/share/gromacs/top/ffgmx.itp<br>Opening library file /usr/share/gromacs/top/ffgmxnb.itp<br>Opening library file /usr/share/gromacs/top/ffgmxbon.itp<br>Opening library file /usr/share/gromacs/top/ff_dum.itp<br>
Opening library file /usr/share/gromacs/top/spc.itp<br>Generated 1284 of the 1485 non-bonded parameter combinations<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>processing coordinates...<br>double-checking input for internal consistency...<br>
Velocities were taken from a Maxwell distribution at 300 K<br>renumbering atomtypes...<br>converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/share/gromacs/top/aminoacids.dat<br>
There are: 216 OTHER residues<br>There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Other...<br>Making dummy/rest group for Acceleration containing 648 elements<br>Making dummy/rest group for Freeze containing 648 elements<br>
Making dummy/rest group for Energy Mon. containing 648 elements<br>Making dummy/rest group for VCM containing 648 elements<br>Number of degrees of freedom in T-Coupling group System is 1293.00<br>Making dummy/rest group for User1 containing 648 elements<br>
Making dummy/rest group for User2 containing 648 elements<br>Making dummy/rest group for XTC containing 648 elements<br>Making dummy/rest group for Or. Res. Fit containing 648 elements<br>Making dummy/rest group for QMMM containing 648 elements<br>
T-Coupling has 1 element(s): System<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...</div>
<div>NOTE 2 [file grompp.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, which might produce artifacts.<br> You might want to consider using PME electrostatics.</div>
<div><br>This run will generate roughly 1 Mb of data<br>writing run input file...</div>
<div>There were 2 notes</div>
<div>There was 1 warning</div>
<div>-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>Source code file: ../../../../src/gmxlib/gmx_fatal.c, line: 481</div>
<div>Fatal error:<br>Too many warnings (1), grompp terminated.<br>If you are sure all warnings are harmless, use the -maxwarn option.<br>-------------------------------------------------------</div>
<div>"And You Will Know That My Name is the Lord When I Lay My Vengeance Upon Thee." (Pulp Fiction)</div>
<div> </div>
<div><br><strong>after executing gmxdump the error is </strong></div>
<p><strong></strong> </p>
<div>gmxdump -s topol.tpr | more <br> :-) G R O M A C S (-:</div>
<div> Go Rough, Oppose Many Angry Chinese Serial killers</div>
<div> :-) VERSION 4.0.7 (-:</div>
<div><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org/">http://www.gromacs.org</a> for more information.</div>
<div> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.</div>
<div> :-) gmxdump (-:</div>
<div>Option Filename Type Description<br>------------------------------------------------------------<br> -s topol.tpr Input, Opt! Run input file: tpr tpb tpa<br> -f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt<br>
-e ener.edr Input, Opt. Energy file: edr ene<br> -cp state.cpt Input, Opt. Checkpoint file<br> -p topol.top Input, Opt. Topology file<br>-mtx hessian.mtx Input, Opt. Hessian matrix<br> -om grompp.mdp Output, Opt. grompp input file with MD parameters</div>
<div>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]nr bool yes Show index numbers in output (leaving them out<br>
makes comparison easier, but creates a useless<br> topology)<br>-[no]sys bool no List the atoms and bonded interactions for the<br> whole system instead of for each molecule type</div>
<div><br>-------------------------------------------------------<br>Program gmxdump, VERSION 4.0.7<br>Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737</div>
<div>Can not open file:<br>topol.tpr<br>-------------------------------------------------------</div>
<div>"I Need Love, Not Games" (Iggy Pop & Kate Pierson)<br></div>
<div><br></div>