AMBER Archive (2009)

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

From: Sean Zhao (sean.r.zhao_at_gmail.com)
Date: Fri May 08 2009 - 22:44:29 CDT

Dear Ray and David,

I really appreciate your help! Thank you!
I have visulized the snapshots via VMD$B!$(Bbut 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 <case_at_biomaps.rutgers.edu>wrote:

> 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.
>
> > # COMPLEX RECEPTOR
> LIGAND
> > 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
>
>
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> 

-- 
La vie.
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