protein structure file (psf)- III

["Nitin Rathore" <>]

Hi,
This is what I generated from CHARMM for the NMA dimer. How can I generate
the same information using Modeller. The suggested "write data" command
gives me the numerical values for the dihedral angles. But I am interested
in the connectivities based on the atom indices....

***** A sample of psf file generated using CHARMM for NMA dimer ********
24 !NATOM
1 NMAD 1 NMA CL 24 -0.270000 12.0110 0
2 NMAD 1 NMA HL1 3 0.900000E-01 1.00800 0
3 NMAD 1 NMA HL2 3 0.900000E-01 1.00800 0
4 NMAD 1 NMA HL3 3 0.900000E-01 1.00800 0
5 NMAD 1 NMA C 20 0.510000 12.0110 0
6 NMAD 1 NMA O 70 -0.510000 15.9990 0
7 NMAD 1 NMA N 54 -0.470000 14.0070 0
8 NMAD 1 NMA H 1 0.310000 1.00800 0
9 NMAD 1 NMA CR 24 -0.110000 12.0110 0
10 NMAD 1 NMA HR1 3 0.900000E-01 1.00800 0
11 NMAD 1 NMA HR2 3 0.900000E-01 1.00800 0
12 NMAD 1 NMA HR3 3 0.900000E-01 1.00800 0
13 NMAD 2 NMA CL 24 -0.270000 12.0110 0
14 NMAD 2 NMA HL1 3 0.900000E-01 1.00800 0
15 NMAD 2 NMA HL2 3 0.900000E-01 1.00800 0
16 NMAD 2 NMA HL3 3 0.900000E-01 1.00800 0
17 NMAD 2 NMA C 20 0.510000 12.0110 0
18 NMAD 2 NMA O 70 -0.510000 15.9990 0
19 NMAD 2 NMA N 54 -0.470000 14.0070 0
20 NMAD 2 NMA H 1 0.310000 1.00800 0
21 NMAD 2 NMA CR 24 -0.110000 12.0110 0
22 NMAD 2 NMA HR1 3 0.900000E-01 1.00800 0
23 NMAD 2 NMA HR2 3 0.900000E-01 1.00800 0
24 NMAD 2 NMA HR3 3 0.900000E-01 1.00800 0

PSF
22 !NBOND: bonds
2 1 3 1 4 1 1 5
5 7 7 9 7 8 10 9
11 9 12 9 5 6 14 13
15 13 16 13 13 17 17 19
19 21 19 20 22 21 23 21
24 21 17 18
36 !NTHETA: angles
2 1 3 2 1 4 2 1 5
3 1 4 3 1 5 4 1 5
1 5 6 1 5 7 6 5 7
5 7 8 5 7 9 8 7 9
7 9 10 7 9 11 7 9 12
10 9 11 10 9 12 11 9 12
14 13 15 14 13 16 14 13 17
15 13 16 15 13 17 16 13 17
13 17 18 13 17 19 18 17 19
17 19 20 17 19 21 20 19 21
19 21 22 19 21 23 19 21 24
22 21 23 22 21 24 23 21 24
34 !NPHI: dihedrals
1 5 7 8 1 5 7 9
1 5 7 9 2 1 5 6
2 1 5 7 3 1 5 6
3 1 5 7 4 1 5 6
4 1 5 7 5 7 9 10
5 7 9 11 5 7 9 12
6 5 7 8 6 5 7 9
8 7 9 10 8 7 9 11
8 7 9 12 13 17 19 20
13 17 19 21 13 17 19 21
14 13 17 18 14 13 17 19
15 13 17 18 15 13 17 19
16 13 17 18 16 13 17 19
17 19 21 22 17 19 21 23
17 19 21 24 18 17 19 20
18 17 19 21 20 19 21 22
20 19 21 23 20 19 21 24
4 !NIMPHI: impropers
7 5 9 8 5 1 7 6
19 17 21 20 17 13 19 18

From: Bozidar Jerkovic
To: Nitin Rathore ; 
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: 
[]On">mailto:]On Behalf Of Nitin
Rathore
Sent: Monday, January 21, 2002 7:10 PM
To: 
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