AMBER Archive (2006)

Subject: Re: AMBER: High Values in MMPBSA

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Thu Oct 12 2006 - 10:36:31 CDT

Dear Shozeb,

to me it looks like the problem is not within MM-PBSA but in the
MD-snapshots used. The vdW-energies are extremely high, so my guess is
that two atoms are too close together and this gives nonsensical results.

Recheck the trajectory you used for close contacts, 'vlimit exceeded'
warnings and high vdW energies.

Regards,

Thomas

> I have just run mm_pbsa_stability.in script and this is the first output that
> I have got from the program. I am getting extremely large numbers. Can any
> one point me in the direction where I can make sense of where I am going
> wrong.
>
> The output numbers are listed below.
>
> # COMPLEX RECEPTOR
> LIGAND
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -41.52 510.07 1214.41 380.65 219.18
> 28.23
> VDW 2871679.52 4061479.31 872210.70 1233743.76 1999534.39
> 2827735.56
> INT 2821232.42 3988262.57 1181076.32 1668829.40 1640169.87

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

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