AMBER Archive (2009)

Subject: RE: [AMBER] Problems in the result of MM_PBSA

From: Ray Luo (
Date: Sat May 09 2009 - 20:36:04 CDT


As Dave suggested, can you run sander manually for one snapshot? Do you see
similar large internal energy terms? Please show us at least the energy
section of the output file.

All the best,

Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562

-----Original Message-----
From: [] On Behalf
Of Sean Zhao
Sent: Friday, May 08, 2009 8:44 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Problems in the result of MM_PBSA

Dear Ray and David,

I really appreciate your help! Thank you!
I have visulized the snapshots via VMD,but nothing abnormal was found. The
receptor doesn't have structural clash. The complex ( receptor and ligand )
also didn't run out of the water box. However, there must be something wrong
with my receptor. Now I wonder whether the program Amber can calculate a
receptor which is a tetramer? My receptor is a homotetramer including four
helices. The helices are bounded together with the non-bonded interaction.

On Fri, May 8, 2009 at 8:45 PM, David A. Case

> On Fri, May 08, 2009, Sean Zhao wrote:
> > I used Amber 9 to simulate a small molecule bound in a protein. After I
> have
> > finished the MM_PBSA, I found the result ( shown below ) was very
> > unreasonable. For instance, the delta VDW, INT, GAS, PBTOT and GBTOT are
> all
> > beyond 10 million. However, no error was reported in the terminal when I
> was
> > running the MM_PBSA. How can I fix this issue? Any response will be
> > appreciated.
> > VDW -550.98 22.86 10037286.88 13997.12 840507.41
> > INT 3434.99 36.17 10647284.69 171501.99 369629.85
> Note that you have completely unreasonably van der Waals and internal
> energies for the receptor. Something has gone very badly wrong with that
> part of the simulation, and you need to find out what it is. Certainly,
> visual examination is an absolute must here, as Ray pointed out. It has
> nothing to do with some small difference between am1-bcc and RESP charges.
> In general: the MM-PBSA scripts are intended to be a bookkeeping aid for
> experienced users, who have well-behaved systems. Everyone should carry
> out
> their first such simlations "by hand", doing each step themselves and
> making
> sure they understand what is going on. Even for experienced users, the
> scripts are weak in catching errors -- everyone who has problems needs to
> have
> (or develop) the ability to critically examine simulations to look for
> problems.
> ...dac
> _______________________________________________
> AMBER mailing list

La vie.
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