Christian Barrett wrote:
>
> 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?
Christian, you are not wrong on this, so I strongly recommend to
incorporate this change to the MODELLER libraries or to additional ad
hoc library (which is better way: you can read this additional library
by READ_TOPOLOGY with ADD... flag = ON)
Hopefully, this will help...
Azat
>
> 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
> >