From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Oct 08 2006 - 12:14:41 CDT
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
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