[gmx-users] more questions

[Daan van Aalten]

Hi Luke

This is going to be quite difficult. Usually the way these topology
builders (like pdb2gmx) work is that they need to be able to identify
certain atoms by their name. For instance, to add the psi torsion
angle between residues X and Y, one needs X_CA,X_C,Y_N,Y_CA for the next
psi angle, between Y and Z, one needs Y_CA,Y_C,Z_N,Z_CA
The problem now is that if you think of your entire complicated 3-amino
acid thingy as "residue" Y, the atoms Y_CA in the first and second psi
angle are *not* the same, and as such you cannot build a .rtp entry for
this.
Once the size limit on PRODRG is gone, one should be able to build entire
topologies for protein which contain as much of these modifications as you
want. Perhaps you can test a small section of your protein (< 100 atoms)
with this chromophore in the middle? If it works I'll try to free some
time to up the size limit to 10000 or so.

cheers

Daan




On Mon, 8 Oct 2001, Luke Czapla wrote:

> On Mon, 8 Oct 2001, David van der Spoel wrote:
> 
> > There may be a simpler way. If you just have a single bond between the two
> > residues you can add it to the specbond database. pdb2gmx will then look
> > for Ser-Gly combinations in bonding distance. So what is the chemical
> > nature of the link?
> > 
> 
> Hi David,
>   The carbonyl of serine 65 forms a bond to the amino group of glycine 67
> forming an imidazole ring and the alpha-beta carbon bond of tyrosene 66 is
> oxidized to a double bond.  The result is a highly conjugated planar
> structure.  My guess is that it will not be simple to implement, but with 
> some guidance on how to modify the .rtp and other necessary files I could 
> post a preliminary definition for this chromophore.  Thank you for your
> help.
> 
> Luke
> 
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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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