Zhiping Xu wrote: > Hi all: > I have a basic question here. I want to simulate a infinite alpha-helix > protein, say alanine represented using a unit cell containning 11 residues. > Now I want to simulate it in GROMACS but don't know how to generate TOP > for the structure, i.e. the connectivity between the 1st residue and > image of 11th residue. Conventional TOP generation process using pdb2gmx > will terminated them rather than fit my need. > Could anyone here give me a hand? Thanks. Select to have no termini in pdb2gmx, and then edit the top file manually. Be careful to add all angles, dihedrals, impropers and pairs.
> Best, > ZP > -- > XU Zhiping, Ph. D > Civil and Environmental Engineering > MIT, Cambridge, MA 02139 > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [email protected] [email protected] http://folding.bmc.uu.se _______________________________________________ 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
