Try "genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro" Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed, forcefields do matter.
On 19/08/2008, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > prasun kumar wrote: > >> dear users >> I am trying to run the simulation fo a protein/DMSO system,Its working >> well till genbox but while running GROMPP I am gettin a fatal error,which is >> atom type 'SD' not found. >> SD is given in the gro & itp file of DMSO. >> what should I do to overcome this problem........ >> I have tried by replacing SD by S,but its of no use >> I should generate a separate top file for DMSO and then include it in the >> topology file generated for protein >> I tried to do this also using PDB2GMX command but again I am gettin error >> related to 'SD' >> > > Which force field are you using? If you look at the .rtp entry (if > present), it will tell you the correct atomic nomenclature. Otherwise, you > have an inconsistency in the atomtypes definition in your topology. > > -Justin > > please help me.......... >> regards &thanx in advance >> >> -- >> PRASUN (ASHOKA) >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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 list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- _ _ (_)(_) (,,) =()= ((__)\ _|L\_______/ The Lab Rats When u r busy judging ppl, you've no time to love'em.. -Nick Vujicic
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