If you use pdb2gmx -ss you can interactively choose whether or not your cysteines are linked, and pdb2gmx will write the .top file with the correct designators.
-Justin Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Hi all, > > I want to make the cysteine residues of my peptide to make a disulphide > bridge with each other. So, what type of cysteine residue should I use? There > are 4 possibilities. CYS, CYSH, CYS1, CYS2. The last two seems to be the same > in respect of atomic charges, bond types but not parameters for dihedral > angles. > > Thanks in advance > Ozge Engin > ================================= > Computational Science & Engineering > Koc University > _______________________________________________ > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.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
