RE: AMBER: Problem while saving .top and .crd files.

From: Ross Walker <>
Date: Mon, 30 Jul 2007 21:28:42 -0700

Hi Anju,
You need to provide parameters for any bonds, angles and dihedrals that you
have in your system that are not in the standard force fields. Where did you
get the atom types for your drug molecule? If you are using analogy to the
underlying amino acid force field then you need to calculate any missing
parameters. If you are new to AMBER without experience of force field
derivation then I suggest you stick to antechamber for you drug molecule and
only once you are completely familiar with things you attempt to determine
your own atom types and ultimately parameters.
See for a
tutorial on antechamber.
>How to overcome dis error nd save d topology and coordinate file?
And please try to avoid text message grammar in email messages when you have
a real keyboard to type on.
Good luck...

|\oss Walker

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From: [] On Behalf Of
Anju Sharma
Sent: Monday, July 30, 2007 20:48
Subject: AMBER: Problem while saving .top and .crd files.

Hello Amber users,

While trying to save .top and .crd files for my drug molecule in xleap i
encounterd following error:
Could not find angle parameter (ex: H-C-C, there are lot more lk dis)
Could not find bond parameter (ex: OH-H, and many more)
Building proper torsion parameters.
Building improper torsion parameters.
  total 4 improper torsions applied.
Building H-bond parameters.
Parameter file was not saved.
How to overcome dis error nd save d topology and coordinate file?

Anju Sharma
Project Fellow, 
NIT, Hamirpur (H.P.) 
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Received on Wed Aug 01 2007 - 06:07:30 PDT
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