<br><br>
<div class="gmail_quote"><br>
<div>Dear Sir,</div>
<div>thanks for your attention. i changed the force filed to ''ffgmx2'' and ''ffG43a1'' but i receive a new fatal error abou ''atom type''.</div>
<div> </div>
<div>for the next suggestion i addes ''ffgmx.hdb'' to the topology file but there was alot of error as you see. what shall i do?</div>
<div> </div>
<div>This is my topology file<br>#define HEAVY_H</div>
<div>; Include forcefield parameters<br>#include "ffgmx.itp"</div>
<div>; Include hydrogen data bank<br>#include "ffgmx.hdb"</div>
<div>; Include protein topology<br>#include "top_A.itp"</div>
<div>; Include protein topology<br>#include "top_B.itp"</div>
<div>; Include ibuprofen topology<br>#include "ib.itp"</div>
<div>; Include water topology<br>#include "spc.itp"</div>
<div><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif</div>
<div>; Include generic topology for ions<br>#include "ions.itp"</div>
<div>[ system ]<br>; Name<br>ibuprofen in HSA</div>
<div>[ molecules ]<br>; Compound #mols<br>Protein_A 3<br>Protein_B 0<br>Na 45</div>
<div>----------------------------------------------<br>this is my command in gromacs: grompp -f em.mdp -c ucell-box.pdb -p HSA.top -o em.tpr<br> :-) G R O M A C S (-:</div>
<div> Good ROcking Metal Altar for Chronical Sinners</div>
<div> :-) VERSION 3.3.3 (-:</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/" target="_blank">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 em.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br>
-c ucell-box.pdb Input Generic structure: gro g96 pdb tpr tpb tpa<br> xml<br> -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<br> xml<br>
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<br> xml<br> -n index.ndx Input, Opt. Index file<br>-deshuf deshuf.ndx Output, Opt. Index file<br> -p HSA.top Input Topology file<br>
-pp processed.top Output, Opt. Topology file<br> -o em.tpr Output Generic run input: tpr tpb tpa xml<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj<br> -e ener.edr Input, Opt. Generic energy: edr ene</div>
<div>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-[no]X bool no Use dialog box GUI to edit command line options<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>-np int 1 Generate statusfile for # nodes<br>
-[no]shuffle bool no Shuffle molecules over nodes<br>-[no]sort bool no Sort molecules according to X coordinate<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>
-load string Releative load capacity of each node on a<br> parallel machine. Be sure to use quotes around<br> the string, which should contain a number for<br>
each node<br>-maxwarn int 10 Number of warnings after which input processing<br> stops<br>-[no]check14 bool no Remove 1-4 interactions without Van der Waals<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>creating statusfile for 1 node...</div>
<div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>WARNING 1 [file em.mdp, line unknown]:<br> Unknown left-hand 'bd-temp' in parameter file</div>
<div>checking input for internal consistency...<br>calling /lib/cpp...<br>In file included from HSA.top:22:<br>top_B.itp:35345:9: warning: no newline at end of file<br>processing topology...<br>ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 1]:<br>
<strong>Incorrect number of atomtypes</strong> for dihedral (1 instead of 2 or 4)<br>ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 2]:<br> Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)<br>
ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 3]:<br> Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)<br>ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 4]:<br>
Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</div>
<div>.</div>
<div>.</div>
<div>.</div>
<div><br>ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 146]:<br> Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)<br>Generated 1284 of the 1485 non-bonded parameter combinations<br>
WARNING 2 [file "top_B.itp", line 35345]:<br> Too few parameters on line (source file toppush.c, line 1168)<br>Excluding 3 bonded neighbours for Protein_A 3<br>Excluding 3 bonded neighbours for Protein_B 0<br>Excluding 1 bonded neighbours for Na 45<br>
processing coordinates...</div>
<div>-------------------------------------------------------<br>Program grompp, VERSION 3.3.3<br>Source code file: grompp.c, line: 469</div>
<div><strong>Fatal error:<br>number of coordinates in coordinate file (ucell-box.pdb, 18400)<br> does not match topology (HSA.top, 17574)<br></strong>-------------------------------------------------------</div>
<div>
<div></div>
<div class="Wj3C7c">
<div><br> </div>
<div class="gmail_quote">On Sun, Dec 14, 2008 at 11:35 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>
<div></div>
<div>nafiseh farhadian wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear Sir,<br>i'm one of the new gmx user. i have a problem with gromacs input file.<br>i'll be thanking if you help me.<br>
i'm working on protein system. i have pdb and itp file. in itp file there are hydrogen atoms but in pdb file no. so when i define top file the number of atoms don't match to each other and i get a fattal error. my forcefield in top file is ''ffgmx forcefield''. i'll be appriciate if you help me.<br>
</blockquote><br></div></div>Don't use ffgmx for new simulations... it's been deprecated for years, and pdb2gmx points this out.<br><br>It's also always appropriate to cite the actual error message you received, since if your interpretation of the problem was totally reliable then you probably wouldn't need to be asking for help.<br>
<br>You might try the protonate utility, or using pdb2gmx on your structure to generate your .top file.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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</blockquote></div><br></div></div></div><br>