Hi,

I tried these commands, but I could not manage to get what I wanted. I guess I didn't clarify my question enough. To put it simply, if I have an arbitrary amino acid sequence, say: ALGAG (ala-lys-gly-ala-gly) and I want to generate the connectivities in this molecule based on CHARMM topology and parameter files. i.e. a protein structure file that list all the bonds, bends, dihedrals and improper torsions as the output how do I go about doing this ?

I have little experience with Modeller, Please let me know how to output this information for any random amino acid sequence of intersest, if it is possible to do with Modellerv6.0.

Thanks,

Nitin

----- Original Message -----

From: Bozidar Jerkovic

To: Nitin Rathore ; modeller_usage@guitar.rockefeller.edu

Cc: Andras Fiser ; Andrej Sali ; Bozidar@Guitar. Rockefeller. Edu

Sent: Tuesday, January 22, 2002 2:34 PM

Subject: RE: protein structure file (psf)

Dear Nitin,

Please check out these commands:

WRITE_MODEL

This command writes the current MODEL to a file in the selected format. If the file format is 'PDB', only the selected atoms are written out when WRITE_ALL_ATOMS = off; otherwise all atoms are written out.

http://salilab.org/modeller/manual/node65.html

especially this one:

WRITE_DATA

This command writes the selected types of data about the MODEL to a corresponding file.

http://salilab.org/modeller/manual/node79.html

WRITE_TOPOLOGY_MODEL

This command writes a residue topology library to the specified file.

http://salilab.org/modeller/manual/node61.html

WRITE_PDB_XREF

This command writes the correspondence between the PDB residue numbers and residue indices for the selected part of the MODEL.

http://salilab.org/modeller/manual/node80.html

Thank you,

Bozidar

MODELLER Team

*****************************************

-----Original Message-----
From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org]On Behalf Of Nitin Rathore
Sent: Monday, January 21, 2002 7:10 PM
To: modeller_usage@salilab.org
Subject: protein structure file (psf)

Hi,

I am a new MODELLER user. I am interested in generating a structure file of the protein of my interest.I was wondering, if there is a way in MODELLER to write down a "CHARMM like .psf " file that lists all the bonds, bends, dihedrals, improper dihedrals etc ( for an all atom model, including hydrgens). Supposedly, the "BUILD MODEL" only generates the 3 D coordinates of the atoms in the model, based on the specified sequence of amino acid and the CHARMM topology and parameter file. But I can not figure out how to output a psf, structure file of my model protein.

Looking for some help,

Thanks in advance,

Nitin