carbohydrate minimisation

From: Mark Forster <>
Date: Tue 07 Nov 2000 17:06:33 +0000

Dear AMBER users

I have been using Amber 6 to model carbohydrates using the published
parameters of Homans and these are included in a suitable frcmod file.
This works fine for simulations in vacuo or with a distance dependent

When trying to used a generalised Born model for solvent, by
setting igb=1, then sander stops with the error message given below.
I presume this is because I have not yet specified GB parameters
for the new atom types in the frcmod file. Which file specifies these
parameters for a given atom type ? The error message is a little strange
in that I do not have a residue named 'WAT' in the molecule, where
could this part of the error message come from ?

Thanks for any help.

The input file is also included below:

     Water definition for fast triangulated model:
     Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
Using modified Bondi radii and Tinker screening parameters
 Unable to find bonded partner for atom 16

# minimization, in GB model solvent
# ntb=0 => non periodic
    maxcyc=1000, imin=1, cut=10.0, igb=1, scee=1.2, ntb=0, ntpr=100,

  Dr Mark J Forster Ph.D.
  Principal Scientist
  Informatics Laboratory
  National Institute for Biological Standards and Control
  Blanche Lane, South Mimms,
  Hertfordshire EN6 3QG, United Kingdom.
  Tel  +44 (0)1707 654753
  FAX  +44 (0)1707 646730
Received on Tue Nov 07 2000 - 09:06:33 PST
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