AMBER Archive (2008)

Subject: RE: AMBER: PBCAL in MM_PBSA

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Fri Aug 08 2008 - 13:27:17 CDT

Hannes,

The raw PBCAL number is in the kT unit in "snapshots_com.all.out" but the
final mmpbsa output is in the kcal unit in "snapshot_statistics.out".

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Hannes Wallnoefer
Sent: Friday, August 08, 2008 7:20 AM
To: amber_at_scripps.edu
Subject: AMBER: PBCAL in MM_PBSA

Hi amber users!

Can anyone tell me tell me, how to get the PBCAL from the output of the
mm_pbsa
tool. To follow the snapshot statistics calculation, i performed a mm_pbsa
calulation on a single set of snapshots (one for the complex, one for the
receptor , and one for the ligand; actually i have done it with the first
snapshot of the ras-raf mm_pbsa tutorial). When i compare the
snapshots_com.all.out-file:

MM
GB
PB
MS
1
 BOND = 730.3907 ANGLE = 1984.0754 DIHED =
2313.9147
 VDWAALS = -1869.5971 EEL = -17231.1931 EGB =
-3192.0635
 1-4 VDW = 895.4560 1-4 EEL = 8527.2834 RESTRAINT =
0.0000
corrected reaction field energy: -5337.748484
surface area = 12542.725
ECAVITY = 12542.725
EDISPER = 0.0000

with the snapshot_statistics.out-file:

# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD MEAN

STD
# ======================= =======================
=======================
ELE -8703.91 0.00 -5617.52 0.00 -2098.02

0.00
VDW -974.14 0.00 -639.93 0.00 -257.26

0.00
INT 5028.38 0.00 3440.78 0.00 1587.60

0.00
GAS -4649.67 0.00 -2816.67 0.00 -767.68

0.00
PBSUR 90.31 0.00 62.98 0.00 38.71

0.00
PBCAL -3181.98 0.00 -2498.16 0.00 -1665.90

0.00
PBSOL -3091.67 0.00 -2435.18 0.00 -1627.19

0.00
PBELE -11885.89 0.00 -8115.67 0.00 -3763.92

0.00
PBTOT -7741.34 0.00 -5251.85 0.00 -2394.86

0.00
GBSUR 90.31 0.00 62.98 0.00 38.71

0.00
GB -3192.06 0.00 -2522.35 0.00 -1661.51

0.00
GBSOL -3101.76 0.00 -2459.37 0.00 -1622.79

0.00
GBELE -11895.97 0.00 -8139.87 0.00 -3759.53

0.00
GBTOT -7751.43 0.00 -5276.04 0.00 -2390.47

0.00

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -988.37 0.00
VDW -76.95 0.00
INT 0.00 0.00
GAS -1065.33 0.00
PBSUR -11.38 0.00
PBCAL 982.08 0.00
PBSOL 970.69 0.00
PBELE -6.30 0.00
PBTOT -94.63 0.00
GBSUR -11.38 0.00
GB 991.79 0.00
GBSOL 980.41 0.00
GBELE 3.42 0.00
GBTOT -84.92 0.00
~

I can follow every calculation or any value, but the PBCAL! Can anybody tell
me
where to read it from?

Kind regards,
Hannes

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