AMBER Archive (2009)

Subject: Re: [AMBER] error in MM PBSA

From: David A. Case (
Date: Sat Apr 04 2009 - 16:16:42 CDT

On Sat, Apr 04, 2009, Vikas Sharma wrote:

> i am using MM PBSA...while save .prm & .inpcrd files for a
> co-crystallised PDB file it showed error that the atom types of
> Chloreine atoms in the ligand were undefined. so i deleted those atoms
> from the PDB and then i could continue.

This sounds dangerous..when you say you deleted "those atoms", which
atoms do you mean?

>    c o-ordinate resetting(SHAKE) can't be accomplished, deviation too   large.
> NITER< NIT, LL, I and J are 0, 1884, 3737, 3339
>  Note: this usuaaly is a symptom of some deeper problem with energetics of the system  "

There is no general answer. You should run a short simulation with
ntpr=1 and look carefully for problems. Did you minimize the structure
first? There are many ways you could get problems with energetics --
it's a good idea to visualize your structures and examine them carefully
to find problems.


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