1. look at MM array and PB array.
2. search for EPB and ELRA= FE using / command in terminal
--= ---amber-bounces.ambermd.org wrote: -----
To: "AMBER Mailing List" <amber.amb= ermd.org>
From: "zgong.hust" <zgong.hust.gmail.com>
Sent by:= amber-bounces.ambermd.org
Date: 04/17/2010 08:49PM
Subject: Re: Re: = [AMBER] problem in MMPBSA
Dear sir:
I fol= lowed 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 S= cience and Technology
Wuhan
Hubei Province
China
&#= 21457;件人： Dima A Sabbah
å‘é€æ—¶&#= 38388;： 2010-04-18 01:09:48
收件人ᦂ= 6; AMBER Mailing List
抄é€ï¼š
主题A= 306; 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
&= nbsp;3. cp mm_pbsa to your home (I typed in terminal :cp -rf
mm_pb= s= a
/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
&n= bsp; 10. Go to your working directory &nb= sp; and t=
ype (I typed
= ; /home/Dima/mm_pbsa/mm_pbsa.pl ./input mm_pbsa.in
&n= bsp; 11. I faced a new problem no data for MM + 0 , I edi= tted
also GB &n bsp;=> [1.0 to 0.0
&= nbsp; The Best of Luck!
&nbs= p;
= ; -----amber-bounces.ambe= rmd.org wrote: -----
To= : "AMBER Mailing List" <amber.ambermd.org>
Fro= m: "= zgong.hust" <zgong.hust.gmail.com>
Sen= t by: amber-bounces.ambermd.= org
Date: 04/17/2010= 10:06AM
Subject: [AMBER] problem in MMPBSA
= ; H= i, all,
When I calculate the bin= ding energy of RNA-small molecule i=
nteraction by
= MM_PBSA in AMBER9. Input file is as following:
PR= EF= IX snapshot
PATH = &nb= sp; ./
#
CO= M= PLEX 1
&nb= sp; RECEPTOR = 1
= LIGAND = &= nbsp; 1
#
COMPT = &nbs= p; ./1y26_a.prmtop RECPT &nbs=
p; &nbs= p; ./1y26.prmtop
LIGPT = &nbs= p; ./a.prmtop
&nb= sp; #
GC &nb= sp; = 0
AS &= nbsp= ; 0
= DC= = 0
= #
MM &nbs= p; 1 GB &nbs= p; 1 P= B
= = ;1
MS &nbs= p; 1#
NM &= nbsp; 0<= BR>#
# PROC &nbs= p; 2 REFE &n= bsp; 0
INDI = 1.0
EXDI = 80.0
= SCALE 2
&= nbsp; LINIT &n= bsp; = 1000
PRBRAD = &n= bsp; 1.4
ISTRNG &= amp;nbs= p; 0.0
RADIOP= T &= nbsp; 0
= ; NPOPT &n= bsp; &nb= sp; 1
CAVITY_SURFTEN 0.= 0072
CAVI= TY_OFFSET = 0.00
#
SURFTEN = = 0.0072
SURFO= FF &= nbsp; 0.00
&= nbsp; #
IGB &= nb= sp; 2
GBSA = = ; 1
&nb= sp; SALTCON = ; &nb= sp; 0.00
EXTDIEL = &= nbsp; 80.0
INTDIEL &nbs= p; = ; 1.0
= ; #
SURFTEN &= nbs= p; 0.0072
SURFOFF = = ; 0.00
when I run th= e mm_pbsa.pl, it shows
Use of uninit= ial= ized value in multiplication (*)
&= nbsp;at
/export/home/gz/soft/amber9/src/mm_pb=sa /mm_pbsa_statistics.pm
line 1336.
= ; Use of uninitialized value in m= u= ltiplication
(*) at
/export/ home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_s=tatistics.pm
&nb= sp; line 1336.
No data for 0+2 = PB PB 0
the output file are like this :
&nb= sp; MM
GB
PB
= MS
1
= = ;BOND = 617.4072 ANGLE = = = 1269.1704
DIHED =
&n= bsp; 1= 818.2919
VDWAAL= S = -1366.1237 EEL &nbs= p; = &n= bsp;
32178.2971 EGB
= &nb= sp; -= 41925.7449
1-4 VDW = 639= .5718 1-4= EEL = -6010.0127 RESTRAINT
= =
&n= bsp; 0.0000
&nbs= p; corrected reaction field energy: -71281.229816<= BR>surfa ce area =
12031.916
ECAVITY= = 12031.916
EDISP= ER = 0.0000
= ; 2
BOND = = 579.3= 947 ANGLE = 1293.0841 &n bsp;DIHED = ; =
= 1823.4181
VDWAALS = -1342= .= 5240 EEL = 32086.1669 EGB = =
-41862.3644
&n= bsp; 1-4 VDW = &nbs= p; 644.4107 &n= bsp;1-4 EEL =
-5959.7021 RESTRAINT = &= nbsp; 0.0000
corrected reaction = field en= ergy: -71145.860423
surface area = = 12105.554
ECAVITY = = 12105.554<= BR> EDISPER = 0.0000
there are = no statistics fi= le
How can I fix this ?
= ; Thank you
2010-04-16
= Zhou Gong
School of Physi= cs
Huazhong University of Science an= d Technology Wuhan
Hubei Province
&nbs= p; China
_______ &= nbsp;
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References
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References
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Received on Sun Apr 18 2010 - 12:00:02 PDT
