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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 -----
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,
Bozidar
MODELLER Team
*****************************************
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
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