Re: value of B column is zero

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Oct 08 2006 - 13:29:13 CDT

This is the way things should come out. If you want to keep your
original beta values, you can do so by transferring them from your
original pdb to the new one in VMD. The beta values don't do much in
NAMD simulations except under very special circumstances, though, such
as simulations with constraints, so this is usually nothing to worry about.
Peter

Dhiraj Srivastava wrote:
> 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
> <mailto: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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