On Sat, Apr 17, 2010 at 1:09 PM, Dima A Sabbah <dsabbah.unmc.edu> wrote:
>
> 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
>
Did you re-run the tests after you made these changes and make sure they
passed? I would advise against making any kind of changes in any source
code without re-running the tests to make sure they all passed (it is the
protocol all developers use when developing/editing 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>
> 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_pbsa/mm_pbsa_statistics.pm
> line 1336.
> Use of uninitialized value in mu ltiplication (*) at
> /export/home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_statistics.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
> _______ ________________________ 5F _______________
> AMBER mailing list
> AMBE R.ambermd.org
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>
>
> References
>
> 1. 3D"
> http://lists.ambermd.org/mailman/listinfo/amber_______________________________________________
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Apr 17 2010 - 14:00:03 PDT
