[gmx-users] regarding ligands in proteins

[Luke Czapla]

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         
>