Hi Zhang:
you can extract energy terms for each snapshots from prefix_com.all.out(or
rec.all.out, lig.all.out) into a seperated file. For example:
1). The content of prefix_com.all.out is:
=====prefix_com.all.out========
MM
PB
MS
1
BOND = 207.2842 ANGLE = 886.4916 DIHED =
2458.2773
VDWAALS = -2609.7641 EEL = -25189.6876 HBOND =
0.0000
1-4 VDW = 1073.6154 1-4 EEL = 12345.0770 RESTRAINT =
0.0000
corrected reaction field energy: -4923.742000
surface area = 14783.808
2
BOND = 205.2730 ANGLE = 882.7424 DIHED =
2452.5204
VDWAALS = -2625.4418 EEL = -25127.6069 HBOND =
0.0000
1-4 VDW = 1072.0818 1-4 EEL = 12354.1791 RESTRAINT =
0.0000
corrected reaction field energy: -5061.096000
surface area = 14620.204
=============================
2). extracted seperated files are as follows:
======prefix_com.1.out=======
MM
PB
MS
1
BOND = 207.2842 ANGLE = 886.4916 DIHED =
2458.2773
VDWAALS = -2609.7641 EEL = -25189.6876 HBOND =
0.0000
1-4 VDW = 1073.6154 1-4 EEL = 12345.0770 RESTRAINT =
0.0000
corrected reaction field energy: -4923.742000
surface area = 14783.808
==============================
=====prefix_com.2.out========
MM
PB
MS
1
BOND = 205.2730 ANGLE = 882.7424 DIHED =
2452.5204
VDWAALS = -2625.4418 EEL = -25127.6069 HBOND =
0.0000
1-4 VDW = 1072.0818 1-4 EEL = 12354.1791 RESTRAINT =
0.0000
corrected reaction field energy: -5061.096000
surface area = 14620.204
=============================
3). doing similar operation for prefix_rec.all.out and prefix_lig.all.out
4). write input file for mm_pbsa_statistics.pl
===prefix_statistics.1.in===
prefix_com.1.out
prefix_rec.1.out
prefix_lig.1.out
============================
5). get statistical results for each snapshot
mm_pbsa_statistics.pl 1 0 prefix_statistics.1.in prefix_statistics.1.out
mm_pbsa_statistics.pl 1 0 prefix_statistics.2.in prefix_statistics.2.out
.....
....
You can write a simple shell script for this job.
Best Regards!
Liu
On Tue, 13 Sep 2005 06:43:13 +0800, Suxin Zheng <sxzheng.u.washington.edu>
wrote:
> Hi,
> Can I output each snapshots' energy term from mm_pbsa, such as PBTOTAL,
> vdw,elec term of delta delta G = com_x - rec_x - lig_x, where x
> represents the snaphosts' number.
> Thanks
> suxin
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--
JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
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Received on Tue Sep 20 2005 - 03:53:02 PDT
