Creating new residue types
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
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
There is also a FAQ on this.
Andrej
Azat Badretdinov wrote: > > 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
-- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali@rockvax.rockefeller.edu; http://salilab.org
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 >
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 > >
participants (3)
-
Andrej Sali -
Azat Badretdinov -
Christian Barrett