Hello, Greetings from Pawan. Topologies for lipids like POP are not available in the topology database in gromacs. So the starting point would be to generate a topology and a gro file for the protein alone as such and then edit the topology to include the .itp files as specifically needed for the lipids.
Regards, Pawan On Fri, May 22, 2009 at 4:42 PM, Samik Bhattacharya <[email protected]>wrote: > hi > i am new to Gromacs. i want to simulate a protein inside a lipid > box(preferably POPC or POPE). i have generated the protein inside the POPC > box complex. But whenever i am going to build the .gro and .top file of that > complex with pdb2gmx an error is creeping in saying "Cant find POP in > residue topology database". it cant recognise the lipid.itp and popc.itp > files which i've already put into the top directory. > plese help me out. > thank you > > ------------------------------ > Explore and discover exciting holidays and getaways with Yahoo! India > Travel Click > here!<http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/> > > _______________________________________________ > gmx-users mailing list [email protected] > 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 >
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