0 coordinates for LES atoms in pdb file after solvation

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Thu Jan 25 2007 - 01:45:32 CST

Hi all
        I am planning to run LES and for that i prepared my pdb and psf file
by following PSFGen manual. in this pdb file i was getting same coordinates
for LES atoms. for example

ATOM 7247 HG2 PRO X2002 11.967 50.579 50.090 0.00 1.00 P
H
ATOM 7248 HG2 PRO X2002 11.967 50.579 50.090 0.00 2.00 P
H
ATOM 7249 HG2 PRO X2002 11.967 50.579 50.090 0.00 3.00 P
H
ATOM 7250 HG2 PRO X2002 11.967 50.579 50.090 0.00 4.00 P
H
ATOM 7251 HG2 PRO X2002 11.967 50.579 50.090 0.00 5.00 P
H
ATOM 7252 HG2 PRO X2002 11.967 50.579 50.090 0.00 6.00 P
H
ATOM 7253 HG2 PRO X2002 11.967 50.579 50.090 0.00 7.00 P
H
ATOM 7254 HG2 PRO X2002 11.967 50.579 50.090 0.00 8.00 P
H
ATOM 7255 HG2 PRO X2002 11.967 50.579 50.090 0.00 9.00 P
H
ATOM 7256 HG2 PRO X2002 11.967 50.579 50.090 0.00 10.00 P
H

for one of the atom of the LES segment.

but after solvating the structure using solvate command, i am getting a pdb
file where all the coordinates of the atoms (LES) except the first one is 0.
for example -

ATOM 7247 HG2 PRO X2002 11.967 50.579 50.090 1.00 0.00 P
H
ATOM 7248 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7249 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7250 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7251 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7252 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7253 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7254 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7255 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P
ATOM 7256 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00 P

This is creating problem when i am trying to minimize the structure. does
anyone know What may be the reason and how to solve this problem. i am using
the following command for solvating my protein.

Solvate prodh.psf prodh.pdb -t 10 -o prodh_wb

-- 
Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211

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