Moedd - Why don't you like interactive commands of make_ndx? It is easy to form any atom groups based on your GRO file content...
Vitaly -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester, Rochester, NY, U.S.A. >> >> Please let me explain my naive procedure to make index file so that you can >> make comment. I have created the top file for a single solvent molecule. >> Then removed [system] , [molecule] directives as well as "#ffgmx.itp". The >> [molecule type] is named 'solvent''. I got a sample itp file from a tutorial >> and then copied the contents of this modified top file into the file with >> itp extention and named it solvent.itp. Then I # included this itp file in >> solute. top file and based on solvated gro file added "solvent 1000" in >> [molecule] directive of solute.top. solvated gro contains residues a,b,c for >> solute and 'SOL' for the solvent. > > That all sounds quite sensible, assuming your solvent is not water. > >> then I issue the command : make_ndx -f solvated.gro -o solvated.ndx which >> lists the residues : > > >> 0 System : 30350 atoms >> 1 a : 10 atoms >> 2 b : 330 atoms >> 3 c : 10 atoms >> 4 SOL : 30000 atoms >> >> I am not getting my default groups according to [moleculetype]. Am I missing >> sth? That I am only getting system index group is becase I am only using >> user defined residues? > > The default index groups rely on the residue names being looked up in a > database of residue types (IIRC in share/top/aminoacids.dat). You'd have to > tweak that for it to work in your case. > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
