[gmx-users] regarding ligands in proteins

[Luke Czapla]

Hi Daan,

  Yes, I renamed it as GLUCOSE everywhere.  I used the PRODRG server.  One
problem I encountered with that .itp (I stripped the header from the .top)
was that atom types HO and OS and CS1 were unknown to the GROMOS force
field, and I'm not sure what to do about this. The other problem as David
noted is that the coordinates arent in the .GRO file.  I guess the
solution to that is to use the GRO output from your PRODRG and paste it
into the conf.gro.  How does that sound?

cheers,
Luke


On Wed, 24 Oct 2001, Daan van Aalten wrote:

> 
> 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 
> 
>         O     C           O     C         Visit the PRODRG server to take 
>         "     |           "     |         the stress out of your topologies!
>   N--c--C--N--C--C--N--C--C--N--C--C--O   
>      |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
>      C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
>        "         
>        O         
>