----- Original Message ----- From: Nitin Rathore To: rathore@cae.wisc.edu Sent: Sunday, February 03, 2002 8:13 PM

Hi, well it seems that the "make_restraints" command does output the connectivities I am interested in. I just ran the default "make_restraints" with the only change being in restraints type from "bond" to "stereo". and it does generated all the bonds, bends, dihedrals and impropers. But I still have some doubts :This is how my top file looks like:

# Example for: MAKE_RESTRAINTS, SPLINE_RESTRAINTS, WRITE_RESTRAINTS

# This will compare energies of bond length restraints expressed # by harmonic potential and by cubic spline.

SET OUTPUT_CONTROL = 1 1 1 1 1

READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '1fas', MODEL_SEGMENT = '1:' '61:' SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ; ALIGN_CODES = ALIGN_CODES '1fas-ini' GENERATE_TOPOLOGY SEQUENCE = '1fas-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE '1fas.ini'

MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = '1fas-1.rsr' ENERGY DYNAMIC_SPHERE = off ENERGY OUTPUT ='VERY LONG' SPLINE_RESTRAINTS SPLINE_RANGE = 5.0, SPLINE_DX = 0.005, SPLINE_SELECT = 3 1 1 CONDENSE_RESTRAINTS WRITE_RESTRAINTS FILE = '1fas-2.rsr' ENERGY

Now my questions, things I still need to figure out: (1): In this case we used the 1fas.atm file as the input. What if I donot have the pdb file available. What if the only information I have to start with is just the amino acid sequence of the protein. So please let me know what changes I need to make in my make_restraints.top file so that it can read in just the sequence and generate connectivities.

(2) I tried making an input file in the PIR format, but it does not work, this top program looks for .pdb or .ent or .atm files only.

(3) I am not very sure if I need to have that " CONDENSE_RESTRAINTS" and ther "SPLINE_RESTRAINTS commands . (4) If my input file is in the form of one letter amino acid code, and if somehow you help me make it work, how do we take care of patching the NTER and the CTER end. (5) That ENERGY OUTPUT ='VERY LONG' that u suggested, I am not sure what it does.

Thanks a lot for your help so far..

Nitin

----- Original Message ----- From: "Bozidar Jerkovic" bozidar@salilab.org To: "Nitin Rathore" rathore@cae.wisc.edu Sent: Saturday, February 02, 2002 10:15 AM Subject: Re: protein structure file (psf)- III

> > Hi, > > Please generate all stereo-chemical restraints, and then write them out > (ENERGY OUTPUT = 'VERY LONG') > > Thanks, > Bozidar > > > On 1/2/02 5:14 PM, "Nitin Rathore" rathore@cae.wisc.edu wrote: > > > 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 > > > >