Dear Jason,
1. I did the modification = to mm_pbsa.pm according to AMBER archive
e-mail reply by Mr.Kshatresh Dut= ta Dubey on Thursday May 28 2009.
2. We patched the bug fix but it= didn't work, please let me know what can
we do?
Thank you,
Dima
-----amber-bounces.ambermd.org wrote: ----= -
To: A= MBER Mailing List <amber.ambermd.org>
From: Jason Swails <jason= .swails.gmail.com>
Sent by: amber-bounces.ambermd.org
Date: 04/17/= 2010 03:53PM
Subject: Re: [AMBER] problem in MMPBSA
On Sat, Apr 17, = 2010 at 1:09 PM, Dima A Sabbah <dsabbah.unmc.edu> wrote:
><= BR>> Hi Zhong,
>
> I encountered t= he same problem and I solved i t. Please follow
the
> fo= llowing 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 _stati= stics.pm_old
> 5. vim mm_pbsa_statistics.pm<= BR>> 6. edit ELRAELE => [1.0
to 0.0
> &nbs= p; 7. edit EPB => [ 1.0 to 0.0
> 8. edit PBNO= NPOL => [1.0 to 0.0
> 9. save ; mm_pbsa_s= tatistics.pm
> 10. Go to your working &nb= sp; 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
>
Did you re-run the tests after you made these changes and = make sure they
passed? I would advise against making any kind of c= hanges in any source
code without re-running the tests to make sure they= all passed (it is the
protocol all developers use when developing/editi= ng the code).
All the best,
Jason
>
> = 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>
> &nbs= p; Sent by: amber-bounces.ambermd. org
> Date: 04/17/20= 10 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:
> &nbs= p; PREF IX snapshot<= BR>> PATH
= ./
> #
> CO MP= LEX 1
> = ; RECEPTOR 1
> = LIGAND &nbs= p; 1
> #
> COMPT &= ;nbs p; ./1y26_a.prmtop
> = RECPT &nbs p; .= /1y26.prmtop
> LIGPT = ./a.prmtop
> #
> &nbs= p; GC &nb sp; &= nbsp; 0
> AS & nbsp; &nb= sp; 0
> DC &nbs= p; 0
> = #
> MM = 1 GB = 1 PB
> ;1
&= gt; MS = ; 1#
> NM &nbs= p; 0< BR>#
> #<= BR>> PROC = 2 REFE &nbs= p;
0
> INDI &n= bsp; 1.0
> EXDI &nbs= p; 80.0
> &nbs= p; SCALE 2
> &= nbsp; LINIT &n bsp; &nb= sp; 1000
> PRBRAD &n= bsp; 1.4
> ISTRNG &nbs = p; 0.0
> RADIOPT &nb= sp; & nbsp; 0
> NPOPT &= nbsp; &n bsp; 1
> = ; CAVITY_SURFTEN 0.0072
> = CAVI TY_OFFSET 0.00
> &nb= sp; #
> SURFTEN &nbs= p; 0.0072
> SURFOFF &= amp; nbsp; 0.00
> #
> = IGB &nb sp; &n= bsp; 2
> GBSA = ; 1
> SALTCON = ; 0.00
> &nbs= p;EXTDIEL & nbsp; 80.0<= BR>> INTDIEL
; &= nbsp; 1.0
> #
> SURFTEN &nbs= p; &nbs p; 0.0072
> &nb= sp; SURFOFF ; 0.00> when I run the
mm_pbsa.pl, it shows
> &= nbsp; Use of uninitial ized value = in multiplication
(*) at
> /ex port/home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_statistics.pm
> &n= bsp; line 1336.
> Use of uni= nitialized value in mu ltiplication (*) & nbsp;at
> /export/home/gz/soft/amber9/src/mm_pb sa/mm_pbsa_statistics.pm
> line 1336.
> = ; No data for 0+2 PB PB 0
> the ou= tput file are like this :
> MM
> GB > PB
> MS
> 1<= BR>> ;BOND = 617= .4072 ANGLE =
1269.1704 DIHED &nbs= p; =
> 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; 0.0= 000
> corrected reaction field energy: -71281.22= 9816< BR>surface area
=
> 12031.916
&g= t; ECAVITY = 12031.916
> ED= ISP ER = 0.0000
> 2
> BOND = = 579.3 947 ANGLE = = ; 1293.0841 DIHED
; =
> &nb= sp; 1823.4181
> VDWAALS = &= nbsp; -1342 .5240 EEL = 32086.1669= EGB
=
> -41= 862.3644
> 1-4 VDW = &nbs p; = 644.4107 1-4 EEL = -5959.7021
RESTRAINT
> = = 0.0000
> corrected react= ion field en ergy: -71145.860423
> surface= area = 12105.554
> ECAVITY = 121= 05.554
> EDISPER = 0.0000
> there= are no statistics fi le
> How can I fix this ?
>= Thank you
> 2010-04-16
> &n= bsp; Zhou Gong
> School of Physics<= BR>> Huazhong University of Science an d
Technology<= BR>> Wuhan
> Hubei Province
> &n= bsp; China
> _______ ________________________
&= nbsp; 5F _______________
> = ; AMBER mailing list
> AMBE R.ambermd.org
>= ; [1][1]http://lists.ambermd.org/mailman/listinfo/amber
&= gt;
>
> References
>
> 1. 3D"
> http://lists. ambermd.org/mailman/listinfo/amber_____________
________________________ 5F= _________
> AMBER mailing list
> AMBER.am= bermd.org
> [2]http://lists.ambermd.org/mailman/listinfo/amber
&g= t;
--
---------------------------------------
Jason M= . Swails
Quantum Theory Project,
University of Florida
Ph.D. Gradu= ate Student
352-392-4032
______________ ________________________ 5F= ________
AMBER mailing list
AMBER.ambermd.org
http= ://lists.ambermd.org/mailman/listinfo/amber
=
References
1. 3D"
http://lists.ambermd.org/mailman/listinfo/amb 2. 3D"
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Received on Sun Apr 18 2010 - 12:30:03 PDT
