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Tutorial-l Mailing List

From: Bharath Rajeswaran (bharathrajeswaran_at_gmail.com)
Date: Fri May 28 2010 - 04:20:58 CDT

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I tried to generate a psf file for glucose using pdb with the force field
file top_all22_sugar.inp . I am a beginner in NAMD. I followed the
instructions in the NAMD tutorial. But I got the following error

reading topology file top_all22_sugar.inp

 Topology file for alpha-D-glucopyranose monomer.
 10/13/94 , Guyan Liang and John Brady

Created by CHARMM version 22 1
building segment U
reading residues from pdb file glu1.pdb
unknown residue type BDGL
unknown residue type
extracted 2 residues from pdb file
Info: generating structure...
unknown residue type BDGL
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.
vmd >

Can some one help me ?

Thanks

Cheers
Bharath.R

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