question on mutate command in NAMD

From: Longzhu Shen (lzshen_at_emails.bjut.edu.cn)
Date: Wed Feb 15 2006 - 16:49:19 CST

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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