Hello Shamik, Going through the membrane protein tutorial will help you to get answers to these questions. The lipid.itp file has to be modified and edited depending on the force fields being used like opls force field or the gromos96 force field. Popc.itp file should also be included in order to include the topology for the POP residues. lipid.itp file is used to include more of interaction parameters.
Regards, Pawan On Fri, May 22, 2009 at 4:58 PM, Samik Bhattacharya <[email protected]>wrote: > Thanks pawan, for helping.... but one problem still remains that is how to > incorporate the .itp file inside the topology file???? and which .itp file > should i include is it the lipid.itp orr POPC.itp?? > thanx for your help > Shamik > > > > > > 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]<http://mc/[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://mc/[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]<http://mc/[email protected]> >> . >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -----Inline Attachment Follows----- > > _______________________________________________ > gmx-users mailing list > [email protected]<http://mc/[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]<http://mc/[email protected]> > . > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ------------------------------ > Bollywood news, movie reviews, film trailers and more! Click > here.<http://in..rd.yahoo.com/tagline_movies_1/*http://in.movies.yahoo.com/?wm=n/> > _______________________________________________ > 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 >
_______________________________________________ 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
