Re: question on mutate command in NAMD

From: surendra negi (negi009_at_yahoo.com)
Date: Wed Feb 15 2006 - 10:58:53 CST

Test following. It was working for me.

 package require psfgen
 topology top_all27_prot_lipid.inp
 
  segment A { pdb fp.pdb
      mutate 2 GLU
             }
  coordpdb fp.pdb A
  writepsf mutated.psf
  guesscoord
  writepdb mutated.pdb
 
sn

--- Longzhu Shen <lzshen_at_emails.bjut.edu.cn> wrote:

> Dear all,
>
> I am trying to mutate the second residue (Val)of a
> peptide to Glu(E) with
> NAME. The script is shown bellow:
>
> ===================================
> package require psfgen
> topology top_all27_prot_lipid.inp
>
> segment A { pdb fp.pdb
> mutate resid 2 GLU
> }
> coordpdb fp.pdb A
> writepsf mutated.psf
> guesscoord
> writepdb mutated.pdb
>
> exit
>
> =====================================
>
> It returned some errors:
>
> =========================================
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to
> start over.
> ERROR: failed while building segment
> reading coordinates from pdb file fpwt.pdb for
> segment A
> Warning: failed to set coordinate for atom N
> ALA:1 A
> Warning: failed to set coordinate for atom CA
> ALA:1 A
> Warning: failed to set coordinate for atom C
> ALA:1 A
> .
> .
> .
> Info: writing psf file fpV2E.psf
> ERROR: failed on writing structure to psf file
> ERROR: failed on guessing coordinates
> Info: writing pdb file fpV2E.pdb
> ERROR: failed on writing coordinates to pdb file
> ============================================
>
> Could anyone give me some help to tackle this
> problem? Many thanks.
>
> with regards,
>
> Longzhu
>

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