AMBER Archive (2008)

Subject: AMBER: something puzzled with mm_pbsa

From: TaoPaul (paultao2008_at_hotmail.com)
Date: Fri Oct 24 2008 - 05:50:04 CDT

Hi all

when I did practise using mm_pbsa.pl to calculate the free energy of the complex ras-raf

provided by amber itself, setting MS=0, PB=1, I found some phenomena puzzled me!

1.there was not area surface term in the ras_raf_II_wt_com.all.out file,
1
 BOND = 693.4575 ANGLE = 1895.7111 DIHED = 1478.8198
 VDWAALS = -1974.0288 EEL = -17194.5212 HBOND = 0.0000
 1-4 VDW = 866.5634 1-4 EEL = 7173.9328 RESTRAINT = 0.0000
corrected reaction field energy: -6656.288058
 ECAVITY = 91.5523 EDISPER = 0.0000

and in the final log file the following warning existed

=>> Reading files
    Reading ras_raf_II_wt_com.all.out
    WARNING: Missing SURF for MS in 0 -> Taken from -1
    WARNING: Missing SURF for MS in 1 -> Taken from 0
    WARNING: Missing SURF for MS in 2 -> Taken from 1
    WARNING: Missing SURF for MS in 3 -> Taken from 2
   
 although the situation mentioned above existed, the ras_raf_II_wt_statistics.out file

could still be obtained.
# MEAN STD
# =======================
ELE -9997.78 32.24
VDW -1109.05 8.26
INT 4062.38 24.18
GAS -7044.46 34.03
PBSUR 91.55 0.13
PBCAL -4003.86 31.15
PBSOL -3912.32 31.17
PBELE -14001.65 31.14
PBTOT -10956.78 20.92

 However, when you set MS=1 or (MS=0, GB=1), the area surface both existed in the

ras_raf_II_wt_com.all.out file.

2. when you tried to calculate the binding free energy, setting MS=0 PB=1 the procedure

stopped at
"=>> Calc delta from raw data
    No data for 0+0 MS SURF 0 "

Now my questions are following:
1.Can the PBSA procedure generate the molecular surface automatically? If it can why
it doesn't shown in the ras_raf_II_wt_com.all.out file and give the warning mentioned above

and interrupted the binding energy calculation, if not how does the value of PBSUR in the

ras_raf_II_wt_statistics.out get?

2.what should I do if I want to calculate the binding free energy with MS=0 PB=1. I have to

do it because my system studying have F elements while I don't know the radius parameter.

Best wishes!

Paul Tao

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