AMBER Archive (2006)

Subject: Re: AMBER: regarding PBCAL in MM-PBSA

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Oct 16 2006 - 20:15:20 CDT


Thanks for replying Luo,

Here is my MM_PBSA output.

please let me know if PBCAL values indicate water/counter ion(s) replacement upon ligand binding in the binding site.

best regards,

jenk.

# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= =======================
ELE -893.14 23.16 -402.01 26.65 -74.71 2.19
VDW -164.05 10.33 -122.65 7.64 6.85 2.10
INT 868.03 17.13 751.31 16.56 116.72 5.07
GAS -189.15 24.80 226.65 29.26 48.86 5.30
PBSUR 19.66 0.45 19.38 0.18 5.53 0.03
PBCAL -2850.92 18.55 -3197.02 23.52 -85.84 2.03
PBSOL -2831.25 18.68 -3177.64 23.57 -80.31 2.02
PBELE -3744.05 11.60 -3599.03 10.21 -160.55 0.84
PBTOT -3020.40 16.57 -2950.98 16.29 -31.45 5.05
TSTRA 15.45 0.00 15.37 0.00 13.32 0.00
TSROT 14.76 0.03 14.59 0.04 11.73 0.01
TSVIB 431.61 2.29 381.06 2.72 48.73 0.36
TSTOT 461.82 2.30 411.02 2.76 73.78 0.37

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -416.42 12.74
VDW -48.24 5.15
INT 0.00 0.00
GAS -464.66 15.54
PBSUR -5.25 0.36
PBCAL 431.94 13.17
PBSOL 426.69 12.91
PBELE 15.52 4.51
PBTOT -37.97 4.53
TSTRA -13.23 0.00
TSROT -11.56 0.05
TSVIB 1.82 3.48
TSTOT -22.97 3.52

Ray Luo <rluo_at_uci.edu> wrote: Dear Jenk,

Please provide more information on your calculation. The statistics
output would be a good start.

Best,
Ray

Cenk Andac wrote:

> Dear Amber community,
>
> I was just wondering how one would go about interpretation of PBCAL
> values (in MMPBSA computations) for receptor and complex. PBCAL for my
> receptor has a more negative value than PBCAL for the complex. Does
> this mean that the complex experiences a lower dielectric lattice due
> to some water molecules replaced by the ligand in the binding site?
>
> best regards,
>
> jenk.
>
>
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-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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