[gmx-users] regarding ligands in proteins

[Daan van Aalten]

Hi Luke

Well in that case follow the recipe as provided by David in his reply to
your original message.
If you put your coordinates into PRODRG with EM switched off, neither
the atom names nor the coordinates are changed,
so you can simply use the resulting GROMOS formatted coordinate file and
append to to your GROMACS coordinate file after pdb2gmx. 
Then put the PRODRG GMX
topology into a file that you call (for instance) glucose.itp. Include
that in your protein topology file and you should be done.
Let me know if you (don;t) get it to work

cheers

Daan

On Mon, 8 Oct 2001, Luke Czapla wrote:

> 
> Hi,
> 
>   Thank you for responding Daan.  I am starting with a crystallographic
> complex of glucose with the protein.  I am unsure what you mean by
> specifying my file along with the ffgmx.*, because I dont see any
> command options in the manual pages for something like that for pdb2gmx.
> But yes, this is the situation that I am working with.  So I have
> something like protein.pdb that contains the glucose in it under the ATOM
> section and a glucose.top file generated from PRODRG (input similar to the
> stick figure like your example but taken from the PDB lines as a pyranose
> configuration).
> 
> cheers,
> Luke
> 
> 
> On Mon, 8 Oct 2001, Daan van Aalten wrote:
> 
> > 
> > Hi Luke
> > 
> > It's not clear from your message if you are starting from a
> > crystallographically defined complex of glucose with the glucose binding
> > protein. If so, use the file you got from the PRODRG server, and specify
> > that together with your ffgmx.* when you run pdb2gmx.
> > 
> > If you do not have a complex, you need to use a program like DOCK/AUTODOCK
> > first to "generate" the complex, then run as above.
> > 
> > If you have generated the glucose topology from scratch with PRODRG (i.e.
> > using the ASCII drawing, which is preferred) you can use the attached
> > FORTRAN jiffy to "swap" atomnames after you have approximaetly positioned
> > the PRODRG glucose over the PDB glucose.
> > 
> > hope this helps
> > 
> > Daan
> > 
> > 
> > ##############################################################################
> >  
> > 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         
> > 
> 
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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