Re: value of B column is zero

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Sun Oct 08 2006 - 12:26:57 CDT

Hi Peter
           when i am using pefgen to generate my structure file, I am
getting zero beta values for all the atoms. but in the original pdb files,
from where i am generating my structure, beta values are not zero. they have
some values. is it correct or there is some problem in my psfgen script.

Dhiraj

On 10/8/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> If you need to have non-zero beta values in your pdb, the best way to do
> this is load your pdb file into VMD after running psfgen, set the beta
> values, save a new pdb, and use that one instead. As long as this is all
> you change, the same psf file is still valid.
> Peter
>
> Dhiraj Srivastava wrote:
> > Hi all
> > sorry for the previous mail. actually the problem is in my
> > structure file. when i ma generating the structure file, i am getting
> > the pdb file in which values of B column are zero. my psfgen script is
> > package require psfgen
> >
> > topology top_all27_prot_lipid.rtf
> > topology fad_top.inp
> >
> > pdbalias residue HIS HSE
> > pdbalias atom ILE CD1 CD
> > pdbalias residue HOH TIP3
> >
> > segment A {pdb chain_A.pdb}
> > coordpdb chain_A.pdb A
> >
> > segment B {pdb chain_B.pdb}
> > coordpdb chain_B.pdb B
> >
> >
> > segment F {pdb FAD.pdb}
> > coordpdb FAD.pdb F
> >
> > segment W {
> > auto none
> > pdb water.pdb}
> >
> > pdbalias atom HOH O OH2
> >
> > coordpdb water.pdb
> >
> > #segment T {pdb TFB.pdb}
> > #coordpdb TFB.pdb T
> >
> > guesscoord
> >
> > #multiply 10 T
> >
> > writepdb prodh1.pdb
> > writepsf prodh1.psf
> >
> > exit
> >
> > can anyone suggest me where is the problem. is there any proble in the
> > psfgen script or problem may be in the topology file.
> >
> >
> > --
> > Dhiraj Kumar Srivastava
> > Department of Chemistry
> > University of Missouri-Columbia
> > MO, 65211
> > Ph. no. 001-573-639-0153
>
>

-- 
Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153

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