Re: 0 coordinates for LES atoms in pdb file after solvation

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Thu Jan 25 2007 - 11:24:16 CST

Hi arijit
Do you know any way to generates LES atoms after preparing Structure file
and solvating it. I was generating these atoms using PSFGen.

Dhiraj

On 1/25/07, arijit_r_at_chem.iitkgp.ernet.in <arijit_r_at_chem.iitkgp.ernet.in>
wrote:
>
> Dear Dhiraj,
> after solvating and adding ion ( if there is ion in your system) then
> try to generate the LES atoms.
> arijit
>
> On Thu, 25 Jan 2007, Dhiraj Srivastava wrote:
>
> > 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
Ph. no. 001-573-639-0153

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