VMD-L Mailing List

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Sat Sep 06 2008 - 04:15:25 CDT

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

 ATOM 1 C X 1 -3.039 1.934 -0.283 0.00 0.00 C
ATOM 2 C X 1 -3.189 0.892 0.625 0.00 0.00 C
ATOM 3 C X 1 -2.112 0.042 0.894 0.00 0.00 C
ATOM 4 C X 1 -0.879 0.204 0.276 0.00 0.00 C
ATOM 5 C X 1 -0.733 1.261 -0.643 0.00 0.00 C
ATOM 6 C X 1 -1.812 2.120 -0.917 0.00 0.00 C
ATOM 7 N X 1 0.123 -0.642 0.571 0.00 0.00 N
ATOM 8 C X 1 1.315 -0.482 -0.029 0.00 0.00 C
ATOM 9 C X 1 1.562 0.544 -0.962 0.00 0.00 C
ATOM 10 C X 1 0.512 1.419 -1.262 0.00 0.00 C
ATOM 11 C X 1 2.353 -1.354 0.273 0.00 0.00 C
ATOM 12 C X 1 3.613 -1.234 -0.321 0.00 0.00 C
ATOM 13 C X 1 3.854 -0.212 -1.232 0.00 0.00 C
ATOM 14 C X 1 2.827 0.670 -1.563 0.00 0.00 C
ATOM 15 N X 1 4.671 -2.189 0.006 0.00 0.00 N
ATOM 16 N X 1 -4..299 0.713 1.207 0.00 0.00 N
ATOM 17 H X 1 -3.879 2.612 -0.492 0.00 0.00 H
ATOM 18 H X 1 -2.248 -0.784 1.607 0.00 0.00 H
ATOM 19 H X 1 -1.685 2.949 -1.629 0.00 0.00 H
ATOM 20 H X 1 0.669 2.239 -1.978 0.00 0.00 H
ATOM 21 H X 1 2.175 -2.167 0.992 0.00 0.00 H
ATOM 22 H X 1 4.846 -0.106 -1.696 0.00 0.00 H
ATOM 23 H X 1 3.013 1.474 -2.290 0.00 0.00 H
ATOM 24 C X 1 5.628 -2.116 -0.419 0.00 0.00 C
ATOM 25 C X 1 -5.107 1.352 1.005 0.00 0.00 C
ATOM 26 C X 1 -4.392 -0.073 1.897 0.00 0.00 C
ATOM 27 H X 1 6.081 -1..136 -0.148 0.00 0.00 H
ATOM 28 H X 1 5.550 -2.185 -1.527 0.00 0.00 H
ATOM 29 H X 1 6.270 -2.939 -0.032 0.00 0.00 H
ATOM 30 H X 1 -4.830 2.397 1.270 0.00 0.00 H
ATOM 31 H X 1 -5.986 1.045 1.614 0.00 0.00 H
ATOM 32 H X 1 -5.354 1.307 -0.080 0.00 0.00 H
ATOM 33 H X 1 -5.425 -0.085 2.310 0.00 0.00 H
ATOM 34 H X 1 -4.187 -1.041 1.386 0.00 0.00 H
ATOM 35 H X 1 -3.663 0.071 2.725 0.00 0.00 H
ATOM 36 C X 1 4.407 -3.273 0.925 0.00 0..00 C
ATOM 37 H X 1 3.586 -3.909 0.524 0..00 0.00 H
ATOM 38 H X 1 5.323 -3.895 1.040 0.00 0.00 H
ATOM 39 H X 1 4.096 -2.858 1.910 0.00 0.00 H
END

and pgn file is

package require psfgen
topology top_all22_prot.inp
#pdbalias atom ILE CD1 CD
segment U {pdb ao.pdb}
coordpdb ao.pdb U
guesscoord
writepdb aoq.pdb
writepsf aoq.psf

the error is (obviously) unknown residue as prompted:
$vmd -dispdev text -e cku.pgn
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
Info) Free system memory: 2607MB (86%)
1.4.5
reading topology file top_all22_prot.inp

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> December 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
 All comments to ADM jr. via the CHARMM web site: www.charmm.org
               parameter set discussion forum

Created by CHARMM version 22 1
building segment U
reading residues from pdb file ao.pdb
unknown residue type
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.
vmd >

can anybody suggest me how can i get around with this porblem and how how to choose residue name? 

-- 
Rudra
JRF; SNBNCBS
http://www.bose.res.in/~rudra
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