AMBER Archive (2004)

Subject: AMBER: questions on mm_pbsa

From: Fang, Jianwen (jwfang_at_ku.edu)
Date: Fri May 14 2004 - 13:49:54 CDT

Dear amber users,

I am trying to use mm_pbsa.pl to calculate binding affinity of a
protein-ligand complex. I was able to repeat the whole tutorial and
everything seems OK. However I ran into some problems when I started to
calculate my complex. PB worked just fine but GB apparently did not
work well. I found the following in the log file when I ran binding
study:

=>> Reading files
    Reading sah_417_com.all.out
    Entry 0 PB PB 0 exists -> overwriting
    WARNING: Missing GB for GB in 0 -> Taken from -1
    Entry 0 PB PB 1 exists -> overwriting
    WARNING: Missing GB for GB in 1 -> Taken from 0

In com.all.out file I found follows:
1
 BOND = 2573.8846 ANGLE = 7059.6739 DIHED =
8399.9910
 VDWAALS = -7332.9080 EEL = -65871.6796 EGB =
nan
 1-4 VDW = 3154.7355 1-4 EEL = 37661.6334 RESTRAINT =
0.0000
corrected reaction field energy: 0.0000 kt
 corrected reaction field energy: -17849.06 kt
surface area = 32697.632

I also did stability study and found GB was 0 in this case.

# MEAN STD
# =======================
ELE -27670.16 307.43
VDW -4169.52 46.25
INT 17981.91 84.92
GAS -13857.77 308.59
PBSUR 176.62 25.43
PBCAL -10975.52 202.31
PBSOL -10798.91 197.35
PBELE -38645.68 128.98
PBTOT -24656.68 142.60
GBSUR 234.50 33.78
GB 0.00 0.00
GBSOL 234.50 33.78
GBELE -27670.16 307.43
GBTOT -13623.27 318.96

Could anybody let me know what went wrong?
Thanks in advance,
--Jianwen
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