[gmx-users] (no subject)

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 14 12:58:01 CEST 2003

On Mon, 2003-04-14 at 10:42, Zhili Zuo wrote:
> hello all:
> I want to generate the topology for the ligand. But my ligand is composed of eight residues, six of them are GLU, LEU, ASP, VAL, GLU and PHe, and two of them are non-peptide residues in the middle.
> when I made top file in www.davapc1.bioch.dundee.ac.uk, the hydrogens in all the carboxyl were missing and the coordinate of hydrogen to the nitrogen in the last GLU  is "nan".
> How can I generate the proper topology of my ligand?
You have to create new residues in the force field of your choice. (.rtp
and .hdb file)
See manual.

> Thank you!!
> 2003-04-14
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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