Hi Justin, Thanks for the info. I know that the topologies are provided in that website. But they have used charmm27 ff and converted it to gromacs format. But I want to use gromos96 45a3 ff. I have another question. Suppose I use those topologies for dopc . And for the sugar part, I use gromos96 45a3. Will it create problem when we combine sugar /dopc system? Thanks Chanchal
On Tue, Aug 18, 2009 at 7:46 PM, Justin A. Lemkul <[email protected]> wrote: > > > Chanchal wrote: > >> Hi All, >> I am a novice in gromacs. I want to study sugar/membrane interaction and >> I want to use gromos96 45a3 ff. At first I am planning to simulate dopc >> bilayer + water. I downloaded the pdb file of dopc from the site >> http://www.bioinf.uni-sb.de/RB/ . Then I typed pdb2gmx_d -f dopc.pdb and >> choose gromos96 45a3 force field. But I got the error "Residue 'OLE' not >> found in residue topology database". How can I fix the error? >> > > This happens because pdb2gmx is not magic. See here: > > > http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database > > The website you reference provides suitable topologies for this type of > simulation, making pdb2gmx unnecessary. > > -Justin > > Thanks >> Chanchal >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.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 > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 [email protected] > http://lists.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 >
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