hi, On Tuesday 25 April 2006 22:28, Ashutosh Jogalekar wrote: > Hello > I have three peptide strands with the sequence HHQALVFFA. I am trying > to create a .gro file of these. But I don' want to merge these chains > together, as the N termini are not capped (NH3+) > When I do pdb2gmx, even when I am not using the -merge option, the > program is still merging the chains together. Since they are actually > separate in reality, this is causing many problems, not the least of > which is that the charge on the system is being cited as +1, when it > should be +3. > What should I do to get rid of this problem?
Correct your pdb file, so that each chain got a unique chain identifier, normally i do this with swiss pdb viewer ( http://www.expasy.org/spdbv/) edit - rename current layer Our pdb should look like: ATOM 1 N SER A 1 45.156 8.138 75.085 0.00 0.00 The "A" after the residue name is the chain identifier. > Thanks > Ashutosh Jogalekar > Emory University > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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