Azat,
Am I going about this the wrong way? As I understand it, if I were
to include AMP (for instance) as a BLK residue then its chemical
information is not used in the homology modelling process --- it is only
treated as a rigid body with particular side-chain contacts. But I
expect some of these contacts to change and I didn't think that
BLK residues would have enough information to allow the homology
modelling process to intelligently alter side-chain contacts.
If I am wrong on this, what does one gain by defining new "residues"
in the way that I was planning to do it?
Thanks,
Christian
> Dera Cristian!
>
> I must confess that I never did that myself. But i suggest that you look
> at modlib/top.lib file and create the correspondent entry
>
> RESI ...
>
> for your molecules.
>
> Please refer to CHARMM documentation for more info.
>
> This is not a lot of information but it could be useful for a start from
> the scratch.
>
> Azat.
>
> Christian Barrett wrote:
> >
> > Hello Modeller users,
> >
> > I am building a homology model from a template that contains
> > hetero atoms that I don't want to include as block (BLK) residues.
> > This means that they must exist in the residue type library
> > (modlib/restyp.lib). Before I attempt to create two new library
> > entries, I would like to know if somebody has already done this
> > for the HETATM entries that I am interested in. They are
> >
> > FDP (FRUCTOSE-2,6-BISPHOSPHATE)
> > and
> > AMP (ADENOSINE MONOPHOSPHATE)
> >
> > Thanks,
> > Christian Barrett
>