Dear sir:
I followed you advise to edit the mm_pbsa_statistics.pm, however, in my mm_pbsa_statistics.pm file, there no ELRAELE, EPB and NONPOL, I have used the AMBER 9, what's wrong with it ?
Thank you
2010-04-18
Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China
发件人： Dima A Sabbah
发送时间： 2010-04-18 01:09:48
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] problem in MMPBSA
Hi Zhong,
I encountered the same problem and I solved i= t. Please follow the
following steps:
1. cd $AMBERHOME
2. cd= src
3. cp mm_pbsa to your home (I typed in terminal :cp -rf mm_pb= sa
/home/Dima)
4. cp mm_pbsa_statistics.pm mm_pbsa= _statistics.pm_old
5. vim mm_pbsa_statistics.pm
6. edit ELRAELE => [1.0 to 0.0
7. edit EPB => [= 1.0 to 0.0
8. edit PBNONPOL => [1.0 to 0.0
9. save = ; mm_pbsa_statistics.pm
10. Go to your working directory and t= ype (I typed
/home/Dima/mm_pbsa/mm_pbsa.pl ./input mm_pbsa.in
11. I faced a new problem no data for MM + 0 , I editted also GB &n bsp;=> [1.0 to 0.0
The Best of Luck!
&nbs= p;
-----amber-bounces.ambe= rmd.org wrote: -----
To: "AMBER Mailing List" <amber.ambermd.org>
From: "= zgong.hust" <zgong.hust.gmail.com>
Sent by: amber-bounces.ambermd.= org
Date: 04/17/2010 10:06AM
Subject: [AMBER] problem in MMPBSA
H= i, all,
When I calculate the binding energy of RNA-small molecule i= nteraction by
MM_PBSA in AMBER9. Input file is as following:
PREF= IX snapshot
PATH = ./
#
CO= MPLEX 1
RECEPTOR = 1
LIGAND = 1
#
COMPT &nbs= p; ./1y26_a.prmtop
RECPT &nbs= p; ./1y26.prmtop
LIGPT = ./a.prmtop
#
GC &nb= sp; 0
AS &= nbsp; 0
DC= 0
= #
MM 1 GB 1 PB = ;1
MS 1#
NM 0<= BR>#
#
PROC 2 REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT &n= bsp; 1000
PRBRAD = 1.4
ISTRNG &nbs= p; 0.0
RADIOPT &= nbsp; 0
NPOPT &n= bsp; 1
CAVITY_SURFTEN 0.0072
CAVI= TY_OFFSET 0.00
#
SURFTEN = 0.0072
SURFOFF &= nbsp; 0.00
#
IGB &nb= sp; 2
GBSA = ; 1
SALTCON = ; 0.00
EXTDIEL &= nbsp; 80.0
INTDIEL = ; 1.0
#
SURFTEN &nbs= p; 0.0072
SURFOFF = ; 0.00
when I run the mm_pbsa.pl, it shows
Use of uninitial= ized value in multiplication (*) at
/export/home/gz/soft/amber9/src/mm_pb=sa/mm_pbsa_statistics.pm
line 1336.
Use of uninitialized value in mu= ltiplication (*) at
/export/home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_s=tatistics.pm
line 1336.
No data for 0+2 PB PB 0
the output file are like this :
MM
GB
PB
MS
1
= ;BOND = 617.4072 ANGLE = = 1269.1704 DIHED =
1= 818.2919
VDWAALS = -1366.1237 EEL &nbs= p; = 32178.2971 EGB
= &nb= sp; -41925.7449
1-4 VDW = 639.5718 1-4= EEL = -6010.0127 RESTRAINT =
&n= bsp; 0.0000
corrected reaction field energy: -71281.229816<= BR>surface area =
12031.916
ECAVITY = 12031.916
EDISP= ER = 0.0000
2
BOND = 579.3= 947 ANGLE = 1293.0841 DIHED = ; =
1823.4181
VDWAALS = -1342= .5240 EEL = 32086.1669 EGB = =
-41862.3644
1-4 VDW = &nbs= p; 644.4107 1-4 EEL = -5959.7021 RESTRAINT = 0.0000
corrected reaction field en= ergy: -71145.860423
surface area = 12105.554
ECAVITY = = 12105.554
EDISPER = 0.0000
there are no statistics fi= le
How can I fix this ?
Thank you
2010-04-16
Zhou Gong
School of Physics
Huazhong University of Science an= d Technology
Wuhan
Hubei Province
China
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Received on Sat Apr 17 2010 - 19:00:02 PDT
