[AMBER] problem converting AmbertoDesmond

From: Albert <mailmd2011.gmail.com>
Date: Mon, 16 Apr 2012 20:54:11 +0200

   I am following the guide at : http://ambermd.org/desmond.html and
trying to convert an Amber MD system into Desmond system. It do
generated a .cms file, but what I found is that all the residues are
renamed 'UNK' and we cannot differentiate which one is which one when I
import to VMD or Maestro.... Moreover, I try to run 'build constrain
steps', there are some problems:

Reading maeff file bm-in.cms
Finding constraint terms...

Examining 39656 bonds in ffio_bonds section...
Found 13138 hydrogen groups.
Generating 453 unique AH2 constraint groups.
Generating 167 unique AH3 constraint groups.
Generating 878 unique AH1 constraint groups.
Generating 11640 unique HOH constraint groups.
Traceback (most recent call last):
line 400, in <module>
line 285, in main
     add_constraint_terms(ct, cons)
line 149, in add_constraint_terms
     raise ValueError, "No angle found for atoms %d %d %d" % (aj,ai,ak)
ValueError: No angle found for atoms 4684 4683 4685

thank you very much
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Received on Mon Apr 16 2012 - 12:00:02 PDT
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