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
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
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 ----- 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
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
-
Bozidar Jerkovic -
Nitin Rathore