[gmx-users] regarding ligands in proteins

[Daan van Aalten]

Hi Luke

Did you rename from DRG to Glucose or from DRG to GLC? Is the name of the
molecule in the PRODRG .itp file now the same as in your PDB file? How did
you generate the topology, from the coordinates or with the text drawing?

cheers

Daan


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.
> 
> Luke
> 
> 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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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

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