[gmx-users] regarding ligands in proteins

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 24 08:54:13 CEST 2001

On Tue, 23 Oct 2001, Luke Czapla wrote:

>I was working on this glucose binding protein (see the message below), and
>I included the glucose in the top file and the error I generate upon
>running grompp is that the number of coordinates in the coordinate file
>does not match the topology (the difference is 17, the number of
>molecules in Glucose!). Any ideas why this might happen? I renamed
>the PRODRG output from DRG to Glucose.
Did you also insert the coordinates for your glucose in the conf.gro file?
Since you took it out of the pdb file, pdb2gmx knows nothing about the

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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