AMBER Archive (2001)

Subject: leap and SP2 nitrogen

From: Mark Forster (mforster_at_nibsc.ac.uk)
Date: Mon Feb 26 2001 - 06:07:27 CST

Dear Amber Users

I have been trying to create the prmcrd/prmtop files
for an NAD molecule in AMBER6. To so this I have a PDB
file with the coordinates, then I have created a leap.in
file to set the charges and atom types for each atom.

This seems to work well for all atoms except one.
When I try the to set the type for a SP2 nitrogen,
which should be type N* in the Cornell et al. 1995
force field, the leap.log file shows the following error:

>> set test.1.N12 type N*
set: Improper number of arguments!
usage: set <container> <parameter> <object>
   or: set default <parameter> <value>

It seems to be using the N* as a wildcard. Is anyone
aware of a workaround that allows the N* type to
be set in a leap.in file ?

Mark F

I can send the relevant PDB and leap.in file if anyone
is sufficiently interested. 

--

  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
  E-mail  mforster_at_nibsc.ac.uk