[gmx-users] regarding ligands in proteins

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 7 22:02:48 CEST 2001

On Sun, 7 Oct 2001, Luke Czapla wrote:

>  I am a graduate student working on setting up a simulation of a
>glucose-binding protein.  The glucose is not covalently linked.  I have a
>topology file for the glucose using the PRODRG server and a modified PDB
>file for the protein without the glucose residue as well as the original
>one with the glucose labeled GLC.
>  Has anyone had experience with a system similar to this?  I'd like to
>place the glucose inside the protein before energy minimization and I have
>looked all through the documentation for genbox and pdb2gmx and found
>nothing to do this.  Any help would be greatly appreciated!
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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