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 ; modeller_usage@salilab.org 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: 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