Subject: CCL:about generating NAMD PSF file

From: "xiongying99" <xiongying99-.at.-fescomail.net>
Date: Thu, 13 Nov 2003 22:38:56 +0000

Dear Sir,
 I tried to use NAMD program to do a MD with an enzyme. When I generate the 
PSF file(run a command: vmd -dispdev text -e *.pgn), I get the following 
error information:
 -----------------------------------------------------------------
ding coordinates from pdb file dpma2p.pdb for segment U
Warning: failed to set coordinate for atom O     ARG:363          U
Warning: failed to set coordinate for atom OXT   ARG:363          U
Warning: failed to set coordinate for atom O1    CBX:169          U
Warning: failed to set coordinate for atom O2    CBX:169          U
Info: guessing coordinates for 2549 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1  ALA:35   U
Warning: poorly guessed coordinate for atom HT2  ALA:35   U
Warning: poorly guessed coordinate for atom HT3  ALA:35   U
Warning: poorly guessed coordinate for atom OT1  ARG:363          U
Warning: poorly guessed coordinate for atom OT2  ARG:363          U
write: dpma.pdb is not logged in
child process exited abnormally
write: dpma.psf is not logged in
child process exited abnormally
 ------------------------------------------------------------------ 

The program implied that it failed to set coordinate for atom O1 and O2 of 
CBX, OXT and O of ARG. Maybe CBX is not a residue, so I need make topology 
and parameter files by myself. However I am surprised why fail to set 
coordinate for O of ARG? The relevant data in pdb file are as follows:
 ------------------------------------------------------------------- 

ATOM   2504  N   ARG A 363      41.396  15.455  11.857  1.00 48.54
ATOM   2505  CA  ARG A 363      42.465  16.448  11.632  1.00100.00
ATOM   2506  C   ARG A 363      42.189  17.560  10.606  1.00100.00
ATOM   2507  O   ARG A 363      41.746  17.235   9.491  1.00 91.41
ATOM   2508  CB  ARG A 363      43.810  15.791  11.367  1.00100.00
ATOM   2509  CG  ARG A 363      44.961  16.745  11.606  1.00100.00
ATOM   2510  CD  ARG A 363      46.290  16.228  11.087  1.00 99.83
ATOM   2511  NE  ARG A 363      47.418  16.656  11.939  1.00100.00
ATOM   2512  CZ  ARG A 363      48.684  16.372  11.632  1.00100.00
ATOM   2513  NH1 ARG A 363      49.011  15.651  10.514  1.00100.00
ATOM   2514  NH2 ARG A 363      49.680  16.805  12.467  1.00100.00
ATOM   2515  OXT ARG A 363      42.443  18.761  10.918  1.00100.00
ATOM   2516  C   CBX A 169      46.148  -4.112  26.276  1.00 23.92
ATOM   2517  O1  CBX A 169      47.170  -3.732  26.821  1.00 13.49
ATOM   2518  O2  CBX A 169      45.286  -4.887  26.831  1.00 15.89
 -------------------------------------------------------------------
Thank you very much! 

 ----------------------------------------------------------------
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From: Giulio Vistoli <giulio.vistoli*at*unimi.it>
Date: Fri, 14 Nov 2003 10:21:18 +0100

You can generate the .psf file for namd program for protein as well as small organic compounds using VEGA (www.ddl.unimi.it)

Giulio Vistoli

_________________________
Giulio Vistoli
Istituto di Chimica Farmaceutica e Tossicologica
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Tel. +39-02-50317545
Fax +39-02-50317565
giulio.vistoli*at*unimi.it
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