AMBER Archive (2009)

Subject: Re: [AMBER] Minimization error on protonated system? Please help. Thanks!

From: David A. Case (
Date: Thu May 28 2009 - 10:17:59 CDT

On Thu, May 28, 2009, Haizhen Zhong wrote:

> I put a +1 charge H close to the carbonyl group

The details of exactly how you did this are important. I suspect that this
charged hydrogen is coming very close (or gets directly on top of) some
negatively charged atom, so that the EEl blows up:

> VD= WAALS = 3516.8043 EEL = ************* HBOND

You should look at the structure of your system right before it blows up to
see if something like this is happening.

But the whole setup seems bizarre: what exactly are you trying to calculate?
TI was designed to compute differences between real chemical states. What is
the purpose of adding a "point charge H" somewhere? What are the force field
parameters of this "H"?


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