psfgen: more problem

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Mon Sep 08 2008 - 13:30:31 CDT

As i wrote in earlier mail, the problem is also happenning for DNA
molecules as well> the 1LAE structure is also giving the error like

$ 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: 2114MB (69%)
1.4.5
reading topology file top_all27_na.rtf

  \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File ////
  \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
   Alexander D. MacKerell Jr. and Nicolas Foloppe
                     December, 2003
All comments to ADM jr. via the CHARMM web site: www.charmm.org
               parameter set discussion forum

Created by CHARMM version 27 1
aliasing residue A to ADE
aliasing residue C to CYT
aliasing residue T to THY
aliasing residue G to GUA
building segment U
reading residues from pdb file la.pdb
unknown residue type C A
extracted 1 residues from pdb file
Info: generating structure....
unknown residue type C A
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.

my pgn file is :
  package require psfgen
  topology top_all27_na.rtf
  pdbalias residue A ADE
  pdbalias residue C CYT
  pdbalias residue T THY
  pdbalias residue G GUA
  #pdbalias atom ILE CD1 CD
  segment U {pdb la.pdb}
  coordpdb la.pdb U
  guesscoord
  writepdb aoq.pdb
  writepsf aoq.psf

part of pdb(pdb code:1LAE) file is added as it is too big to copy here. the problem is its not "understanding". A,T,G,C . why it is so?
CRYST1 1.000 1..000 1.000 90.00 90.00 90.00 P 1 1
ATOM 1 O5' C A X 1 1.477 -17.625 15.716 1.00 0.69 O
ATOM 2 C5' C A X 1 2.783 -18.207 15.687 1.00 0.69 C
ATOM 3 C4' C A X 1 3.875 -17.138 15.666 1.00 0.59 C
ATOM 4 O4' C A X 1 3.727 -16.259 14.515 1.00 0.53 O
ATOM 5 C3' C A X 1 3.793 -16.250 16.893 1.00 0.55 C
ATOM 6 O3' C A X 1 5.095 -15.838 17.309 1.00 0.50 O
ATOM 7 C2' C A X 1 2.990 -15.075 16..428 1.00 0.50 C
ATOM 8 C1' C A X 1 3.387 -14.921 14.972 1.00 0.46 C
ATOM 9 N1 C A X 1 2.287 -14.338 14.161 1.00 0.45 N
ATOM 10 C2 C A X 1 2.599 -13.276 13.317 1.00 0.38 C
ATOM 11 O2 C A X 1 3.743 -12.824 13.280 1.00 0.32 O
ATOM 12 N3 C A X 1 1.607 -12.752 12.545 1.00 0.39 N
ATOM 13 C4 C A X 1 0.361 -13.240 12.597 1.00 0.46 C
ATOM 14 N4 C A X 1 -0.584 -12.704 11.824 1.00 0.47 N
ATOM 15 C5 C A X 1 0.032 -14.326 13.463 1.00 0.54 C
ATOM 16 C6 C A X 1 1.015 -14.843 14.223 1.00 0.53 C
ATOM 17 H5' C A X 1 2.876 -18.828 14.795 1.00 0.73 H
ATOM 18 H5'' C A X 1 2.914 -18.832 16.570 1.00 0.74 H
ATOM 19 H4' C A X 1 4.855 -17.618 15.627 1.00 0.59 H
ATOM 20 H3' C A X 1 3.275 -16.768 17.703 1.00 0.61 H
ATOM 21 H2' C A X 1 1.921 -15.290 16.521 1.00 0.55 H
ATOM 22 H2'' C A X 1 3.251 -14.182 16.993 1.00 0.45 H
ATOM 23 H1' C A X 1 4.278 -14.279 14.907 1.00 0.40 H
ATOM 24 H41 C A X 1 -0.359 -11.936 11.209 1.00 0.43 H
ATOM 25 H42 C A X 1 -1.526 -13.066 11.855 1.00 0.53 H
ATOM 26 H5 C A X 1 -0.982 -14.724 13.508 1.00 0.61 H
ATOM 27 H6 C A X 1 0.792 -15.671 14.895 1.00 0.61 H
ATOM 28 HO5' C A X 1 1.408 -17.120 16.529 1.00 1.15 H
ATOM 29 P G A X 2 5.349 -15.262 18.787 1.00 0.51 P
ATOM 30 OP1 G A X 2 6.454 -16.030 19.404 1.00 0.55 O
ATOM 31 OP2 G A X 2 4.046 -15.151 19.481 1.00 0.57 O
ATOM 32 O5' G A X 2 5.879 -13.777 18.466 1.00 0.42 O
ATOM 33 C5' G A X 2 7.050 -13..583 17.665 1.00 0.36 C
ATOM 34 C4' G A X 2 7.122 -12.167 17.097 1.00 0.31 C
ATOM 35 O4' G A X 2 6.040 -11.901 16.159 1.00 0.28 O
ATOM 36 C3' G A X 2 7.016 -11.115 18.195 1.00 0.32 C
ATOM 37 O3' G A X 2 8.004 -10.099 18.010 1.00 0.30 O
ATOM 38 C2' G A X 2 5.633 -10.554 18.039 1.00 0.32 C
ATOM 39 C1' G A X 2 5.358 -10.689 16.565 1.00 0.28 C
ATOM 40 N9 G A X 2 3.908 -10.747 16.272 1.00 0.28 N
ATOM 41 C8 G A X 2 2.914 -11.439 16.888 1.00 0.36 C
ATOM 42 N7 G A X 2 1.724 -11.340 16.400 1.00 0..34 N
ATOM 43 C5 G A X 2 1.927 -10.472 15.326 1..00 0.23 C
ATOM 44 C6 G A X 2 0.997 -9.963 14.383 1.00 0.17 C
ATOM 45 O6 G A X 2 -0.210 -10.183 14.307 1.00 0.19 O
ATOM 46 N1 G A X 2 1.611 -9.118 13.467 1.00 0.13 N
ATOM 47 C2 G A X 2 2.955 -8.799 13.456 1.00 0.14 C
ATOM 48 N2 G A X 2 3.357 -7.960 12.501 1.00 0.20 N
ATOM 49 N3 G A X 2 3.836 -9.276 14.339 1.00 0.15 N

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