[gmx-users] Generate topology for infinite alpha helix with pbc?

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 13 20:56:09 CEST 2009

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
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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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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