Quoting Moutusi Manna <[EMAIL PROTECTED]>: > thanks for reply.I want to perform simulation of popc membrane. > Steps which i have done are as follows: > 1. download popc128a.pdb, popc.it,lipids.itp > (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) > 2. download ffgmx_lipids files > 3.convert POPC of .top & popc.itp into POP as in popc.gro > 4. #include "ffgmx.itp" > #include "lipid.itp" > #include "popc.itp" > #include "ffgmxnb.itp" > #include "ffgmxbon.itp"
These last two lines should already be included in ffgmx.itp, and including them twice may cause some headaches. > ................ in my .top file. > > Now when I perform > pdb2gmx -ff gmx -f popc128a.pdb -o popc.gro -p popc.top > it shows the error that"Residue 'POP' not found in residue topology > database". > I think that's because of the fact that ffgmx.rtp do not > contain "POP" residue ,but it has DPPC residue. > Plz suggest how can i solve this problem. > thanks. Use editconf to convert between .pdb and .gro. You only need pdb2gmx if you don't have a .top file, but Prof. Tieleman has kindly provided this for you already, in the form of lipid.itp and popc.itp. -Justin ====================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://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
