From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Sep 07 2008 - 13:50:39 CDT

On Sat, 6 Sep 2008, Rudra Banerjee wrote:

RB> dear friends,

rudra,

RB> i need to generate psf file of cridine orange. i have managed to get
RB> the pdb and managed to create the pdb without H atoms as told in
RB> tutorial. but whem i am trying to create psf file, its showing
RB> error.

what you are doing cannot work. to understand why, you first have
to understand how the construnctions of .psf files works. tools
like psfgen read a database of known residues and then match the
residue and atom names of those residues agains entries in the
pdb file. this works quite well with proteins, since they are built
from just a limited number of amino acids and the atom names in
the pdb data bank files follow certain naming conventions, which
makes it easy to match them against the database. if you'd create
a pdb file of, say, alanine without giving it the proper residue
name and following the atom naming conventions, psfgen would
fail just as well. to build a proper .psf file for an unusual
molecule, you'll have to work a _lot_ harder and first learn
the structure of force fields and their data base file, so you
can write custom entries and know which atom type to match with
the individual atoms in your molecule and then determine what
(partial) charge you'll to attribute each atom in your molecule,
so that it behaves properly. there are some tutorials on the
NAMD home page that can help you with that, but ultimately,
you'll have to dig through some original literature on force-field
parametrization and practice a bit, too. i would perhaps start
with a non-standard molecule that has already been parametrized
and see if you would derive similar enough parameters...

cheers,
    axel.

RB> py pdb file is :
RB>
RB> ATOM 1 C X 1 -3.039 1.934 -0.283 0.00 0.00 C
RB> ATOM 2 C X 1 -3.189 0.892 0.625 0.00 0.00 C
RB> ATOM 3 C X 1 -2.112 0.042 0.894 0.00 0.00 C
RB> ATOM 4 C X 1 -0.879 0.204 0.276 0.00 0.00 C
RB> ATOM 5 C X 1 -0.733 1.261 -0.643 0.00 0.00 C
RB> ATOM 6 C X 1 -1.812 2.120 -0.917 0.00 0.00 C
RB> ATOM 7 N X 1 0.123 -0.642 0.571 0.00 0.00 N
RB> ATOM 8 C X 1 1.315 -0.482 -0.029 0.00 0.00 C
RB> ATOM 9 C X 1 1.562 0.544 -0.962 0.00 0.00 C
RB> ATOM 10 C X 1 0.512 1.419 -1.262 0.00 0.00 C
RB> ATOM 11 C X 1 2.353 -1.354 0.273 0.00 0.00 C
RB> ATOM 12 C X 1 3.613 -1.234 -0.321 0.00 0.00 C
RB> ATOM 13 C X 1 3.854 -0.212 -1.232 0.00 0.00 C
RB> ATOM 14 C X 1 2.827 0.670 -1.563 0.00 0.00 C
RB> ATOM 15 N X 1 4.671 -2.189 0.006 0.00 0.00 N
RB> ATOM 16 N X 1 -4..299 0.713 1.207 0.00 0.00 N
RB> ATOM 17 H X 1 -3.879 2.612 -0.492 0.00 0.00 H
RB> ATOM 18 H X 1 -2.248 -0.784 1.607 0.00 0.00 H
RB> ATOM 19 H X 1 -1.685 2.949 -1.629 0.00 0.00 H
RB> ATOM 20 H X 1 0.669 2.239 -1.978 0.00 0.00 H
RB> ATOM 21 H X 1 2.175 -2.167 0.992 0.00 0.00 H
RB> ATOM 22 H X 1 4.846 -0.106 -1.696 0.00 0.00 H
RB> ATOM 23 H X 1 3.013 1.474 -2.290 0.00 0.00 H
RB> ATOM 24 C X 1 5.628 -2.116 -0.419 0.00 0.00 C
RB> ATOM 25 C X 1 -5.107 1.352 1.005 0.00 0.00 C
RB> ATOM 26 C X 1 -4.392 -0.073 1.897 0.00 0.00 C
RB> ATOM 27 H X 1 6.081 -1..136 -0.148 0.00 0.00 H
RB> ATOM 28 H X 1 5.550 -2.185 -1.527 0.00 0.00 H
RB> ATOM 29 H X 1 6.270 -2.939 -0.032 0.00 0.00 H
RB> ATOM 30 H X 1 -4.830 2.397 1.270 0.00 0.00 H
RB> ATOM 31 H X 1 -5.986 1.045 1.614 0.00 0.00 H
RB> ATOM 32 H X 1 -5.354 1.307 -0.080 0.00 0.00 H
RB> ATOM 33 H X 1 -5.425 -0.085 2.310 0.00 0.00 H
RB> ATOM 34 H X 1 -4.187 -1.041 1.386 0.00 0.00 H
RB> ATOM 35 H X 1 -3.663 0.071 2.725 0.00 0.00 H
RB> ATOM 36 C X 1 4.407 -3.273 0.925 0.00 0..00 C
RB> ATOM 37 H X 1 3.586 -3.909 0.524 0..00 0.00 H
RB> ATOM 38 H X 1 5.323 -3.895 1.040 0.00 0.00 H
RB> ATOM 39 H X 1 4.096 -2.858 1.910 0.00 0.00 H
RB> END
RB>
RB> and pgn file is
RB>
RB> package require psfgen
RB> topology top_all22_prot.inp
RB> #pdbalias atom ILE CD1 CD
RB> segment U {pdb ao.pdb}
RB> coordpdb ao.pdb U
RB> guesscoord
RB> writepdb aoq.pdb
RB> writepsf aoq.psf
RB>
RB> the error is (obviously) unknown residue as prompted:
RB> $vmd -dispdev text -e cku.pgn
RB> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
RB> Info) http://www.ks.uiuc.edu/Research/vmd/
RB> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
RB> Info) Please include this reference in published work using VMD:
RB> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
RB> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
RB> Info) -------------------------------------------------------------
RB> Info) Multithreading available, 2 CPUs detected.
RB> Info) Free system memory: 2607MB (86%)
RB> 1.4.5
RB> reading topology file top_all22_prot.inp
RB>
RB> >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
RB> >>>>>>>>>>>>>>>>>>>>> December 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
RB> All comments to ADM jr. via the CHARMM web site: www.charmm.org
RB> parameter set discussion forum
RB>
RB> Created by CHARMM version 22 1
RB> building segment U
RB> reading residues from pdb file ao.pdb
RB> unknown residue type
RB> extracted 1 residues from pdb file
RB> Info: generating structure...
RB> unknown residue type
RB> ERROR: failed on end of segment
RB> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
RB>
RB> MOLECULE MISSING! Use resetpsf to start over.
RB>
RB> MOLECULE MISSING! Use resetpsf to start over.
RB>
RB> MOLECULE MISSING! Use resetpsf to start over.
RB>
RB> MOLECULE MISSING! Use resetpsf to start over.
RB> vmd >
RB>
RB>
RB> can anybody suggest me how can i get around with this porblem and how how to choose residue name?
RB>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.