Re: [AMBER] MMPBSA problem binding energy calculation

From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Wed, 2 Jun 2010 10:21:41 +0900

Hello Dr. Bill,

I could see just now, there is some problem with the prmtop file that I
used.... For the first step to extract snapshots I used the MEK_vac.prmtop
file of complex when it was not solvated whereas MD simulation, which
generated mdcrd file, was run on solvated model so i think I should have
used MEK_wat.prmtop file which was generated after I solvated the complex. I
don,t know if this is the problem. I will repeat the calculations this way
and see if the prob is resolved...

Thank you
kamlesh

On Wed, Jun 2, 2010 at 10:05 AM, kamlesh sahu <kamleshsemail.gmail.com>wrote:

> Hello Dr. Bill,
>
> Thank you for your suggestions.
> As a first step, I extracted the snapshots like snapshot_com.crd.1,
> snapshot_com.crd.2 ... and so on. I tried loading these with MEK_vac.prmtop
> file in VMD, but I can not see anything in VMD OpenGL Display (Is that what
> you were asking me to visualize ?... does this mean my first step was wrong
> ?).
>
> I have included Zinc as a part of receptor as all the 3 Zn ions are away
> from the ligand. I visualized the re-imaged mdcrd files generated after
> heat-up MD (20ps) and Production MD (100ps). The re-imaged mdcrd file in VMD
> looks fine.
>
>
>
> Thank you
> Best Regards,
> kamlesh
>
> On Tue, Jun 1, 2010 at 8:02 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
>
>> Have you tried visualizing the coordinate files that were generated in the
>> first step? You should do this first to verify that you are creating
>> coordinate files that exactly matchup with your prmtop files the way you
>> want. For example, if you include the zinc ions in the prmtop(s), then
>> they
>> need to be included in your atom numbers and in the correct location
>> (ligand
>> or receptor).
>>
>> -Bill
>>
>> On Tue, Jun 1, 2010 at 5:42 AM, kamlesh sahu <kamleshsemail.gmail.com
>> >wrote:
>>
>> > Dear amber users,
>> >
>> >
>> > Hello
>> > I need your help.
>> >
>> >
>> >
>> > I wish to calculate binding free energy for a complex. So I prepared
>> prmtop
>> > files for the ligand and receptor (pdb contains 3 zinc ions). I also run
>> MD
>> > simulation with the solvated complex structure containing ligand. When I
>> > use
>> > mm_pbsa.pl to calculate binding energy it gives following error-
>> >
>> >
>> >
>> > /home/xtal/amber_10_install/exe/sander -O -i sander_com.in -o
>> > sander_com.1.out -c ./snapshot_com.crd.1 -p ./MEK_vac.prmtop not
>> successful
>> >
>> >
>> >
>> >
>> >
>> >
>> > The input files are ---
>> > The extract_coords.mmpbsa file is as follows-
>> >
>> >
>> > .GENERAL
>> > PREFIX snapshot
>> > PATH ./
>> > COMPLEX 1
>> > RECEPTOR 1
>> > LIGAND 1
>> > COMPT ./MEK_vac.prmtop
>> > RECPT ./MEK_minus_SAM_vac.prmtop
>> > LIGPT ./SAM_vac.prmtop
>> > GC 1
>> > AS 0
>> > DC 0
>> > MM 0
>> > GB 0
>> > PB 0
>> > MS 0
>> > NM 0
>> > .MAKECRD
>> > BOX YES
>> > NTOTAL 3560
>> > NSTART 1
>> > NSTOP 200
>> > NFREQ 1
>> > NUMBER_LIG_GROUPS 1
>> > LSTART 3359
>> > LSTOP 3385
>> > NUMBER_REC_GROUPS 1
>> > RSTART 1
>> > RSTOP 3355
>> > .TRAJECTORY
>> > TRAJECTORY ./md1.mdcrd
>> > TRAJECTORY ./md2.mdcrd
>> > .PROGRAMS
>> >
>> > I TRIED WITH SOME MODIFICATIONS OF THIS FILE ALSO.... LIKE IF I INCLUDE
>> Zn
>> > IONS, RSTOP=3358,... but again the same error.
>> >
>> > The binding_energy.mmpbsa file -
>> >
>> > .GENERAL
>> > PREFIX snapshot
>> > PATH ./
>> > COMPLEX 1
>> > RECEPTOR 1
>> > LIGAND 1
>> > COMPT ./MEK_vac.prmtop
>> > RECPT ./MEK_minus_SAM_vac.prmtop
>> > LIGPT ./SAM_vac.prmtop
>> > GC 0
>> > AS 0
>> > DC 0
>> > MM 1
>> > GB 1
>> > PB 1
>> > MS 1
>> > NM 0
>> > .PB
>> > PROC 2
>> > REFE 0
>> > INDI 1.0
>> > EXDI 80.0
>> > SCALE 2
>> > LINIT 1000
>> > PRBRAD 1.4
>> > ISTRNG 0.0
>> > RADIOPT 0
>> > NPOPT 1
>> > CAVITY_SURFTEN 0.0072
>> > CAVITY_OFFSET 0.00
>> > SURFTEN 0.0072
>> > SURFOFF 0.00
>> > .MM
>> > DIELC 1.0
>> > .GB
>> > IGB 2
>> > GBSA 1
>> > SALTCON 0.00
>> > EXTDIEL 80.0
>> > INTDIEL 1.0
>> > SURFTEN 0.0072
>> > SURFOFF 0.00
>> > .MS
>> > PROBE 0.0
>> > .PROGRAMS
>> >
>> > First I extracted the snapshots using command -
>> >
>> > $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
>> >
>> > Then I used following command to calculate binding energy -
>> >
>> > $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>> >
>> > I got this error --->
>> >
>> > /home/xtal/amber_10_install/exe/sander -O -i sander_com.in -o
>> > sander_com.1.out -c ./snapshot_com.crd.1 -p ./MEK_vac.prmtop not
>> successful
>> >
>> >
>> >
>> > Kindly suggest me the ways to improve my calculation.
>> >
>> >
>> >
>> > Thank you
>> >
>> > Regards,
>> >
>> > kamlesh
>> >
>> >
>> > --
>> > Kamlesh Kumar Sahu
>> > wako-shi (saitama)
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Bill Miller III
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-6715
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Kamlesh Kumar Sahu (Ph.D. student)
> Dept. of applied chemistry, Tohoku University graduate school of
> engineering, Aoba-yama, Sendai
> JAPAN
>



-- 
Kamlesh Kumar Sahu (Ph.D. student)
Dept. of applied chemistry, Tohoku University graduate school of
engineering, Aoba-yama, Sendai
JAPAN
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Received on Tue Jun 01 2010 - 18:30:06 PDT
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