[gmx-users] regarding ligands in proteins

Luke Czapla czapla at rutchem.rutgers.edu
Tue Oct 23 22:08:52 CEST 2001

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.


On Sun, 7 Oct 2001, David van der Spoel wrote:

> This is quite simple. You use give the pdb file without protein to pdb2gmx
> to obtain a protein topology. You have a topology for glucose (and also
> protanated coordinates) from the PRODRG server. Now you have to edit the
> coordinate file using a text editor, you just insert the glucoase after
> the protein. Finally you edit the protein topology file to include after
> the protein but before the water the glucose. Strip off the header from
> the gluocse top. You can also write a line in the protein top:
> #include "glusoce.itp"
> (or whatever you called it).
> One step left: in the [ molecules ] bit at the end you add:
> Protein  1
> Glucose  1
> Note that you may have to change the name in the prodrg topology file.
> >
> >
> >
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> 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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