[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

protein structure file (psf)-II

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.
----- Original Message -----
Sent: Tuesday, January 22, 2002 2:34 PM
Subject: RE: protein structure file (psf)

Dear Nitin,
Please check out these commands:
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.
especially this one:
This command writes the selected types of data about the MODEL to a corresponding file.
This command writes a residue topology library to the specified file.
This command writes the correspondence between the PDB residue numbers and residue indices for the selected part of the MODEL.

Thank you,




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

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,