[gmx-users] make a cyclic peptides

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 28 23:57:50 CET 2002

On Thu, 28 Feb 2002, Yuguang Mu wrote:

>How can I made a topology file of a cyclic peptide in GROMACS,
>by using pdb2gmx ?
did you try? did you check the options?

I did it once long ago, but maybe I just selected none for the termini, 
and then added the missing bonds, angles and dihedrals manually. Don't 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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