VMD-L Mailing List

From: Marcin Wojciechowski (nitramus_at_op.pl)
Date: Thu Jun 09 2005 - 04:52:29 CDT

Hello to All,
Dring preparation of the system for MD I encountered the following
problem:

I created initial psf and pdb file of the system using psfgen with 5
copies of the ligand needed for Locally Enhanced Sampling MD in NAMD.

The fragment of my pdb:

ATOM 1 C18 C130 326 3.254 7.549 18.595 1.00 1.00 IH01
ATOM 2 C18 C130 326 3.254 7.549 18.595 1.00 2.00 IH01
ATOM 3 C18 C130 326 3.254 7.549 18.595 1.00 3.00 IH01
ATOM 4 C18 C130 326 3.254 7.549 18.595 1.00 4.00 IH01
ATOM 5 C18 C130 326 3.254 7.549 18.595 1.00 5.00 IH01
ATOM 6 C1 C130 326 2.969 8.913 18.728 1.00 1.00 IH01
ATOM 7 C1 C130 326 2.969 8.913 18.728 1.00 2.00 IH01
ATOM 8 C1 C130 326 2.969 8.913 18.728 1.00 3.00 IH01
ATOM 9 C1 C130 326 2.969 8.913 18.728 1.00 4.00 IH01
ATOM 10 C1 C130 326 2.969 8.913 18.728 1.00 5.00 IH01
etc.

every atom specified for LES is multiplied 5 times here and the BETA
column designates the number of copy (ant that's ok). However when I
solvate such a pdb using simple "solvate system.psf system.pdb -t 15 -o
system.solv" I get the following output from system.solv.pdb:

ATOM 1 C18 C130 326 3.254 7.549 18.595 1.00 0.00 IH01
ATOM 2 C18 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
ATOM 3 C18 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
ATOM 4 C18 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
ATOM 5 C18 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
ATOM 6 C1 C130 326 2.969 8.913 18.728 1.00 0.00 IH01
ATOM 7 C1 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
ATOM 8 C1 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
ATOM 9 C1 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
ATOM 10 C1 C130 326 0.000 0.000 0.000 -1.00 0.00 IH01
etc.

Here the coords of the copies are reseted to 0.0 also BETA "counters"
and occupancies are set to invalid value.

Is solvate module incompatible with pdb produced with psfgen with LES
copies of the atoms? Anyone encountered similar problem? Any
suggestions?

Best regards, Marcin 

-- 
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Marcin Wojciechowski, MSc
Laboratory of Molecular Modeling 
Department of Pharmaceutical Technology
and Biochemistry
Gdansk University of Technology
Narutowicza St 11/12
80-952 Gdansk
POLAND
tel 4858-3471596
fax 4858-3471144
nitramus_at_hypnos.chem.pg.gda.pl
www.pg.gda.pl/chem/katedry/leki/leki.htm
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