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
Subject: RE: protein structure file
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
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.
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,