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
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-----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