[gmx-users] more questions

[Daan van Aalten]

sorry a typo, Y_CA,Y_C,Z_N,Z_CA = omega of course

On Tue, 9 Oct 2001, Daan van Aalten wrote:

> 
> 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 
> 
>         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         
> 
> 


##############################################################################
 
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