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

From: arijit_r_at_chem.iitkgp.ernet.in
Date: Thu Jan 25 2007 - 03:11:44 CST

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
>
>

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