Re: [AMBER] MMPBSA problem binding energy calculation

From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Wed, 2 Jun 2010 10:05:10 +0900

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
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Received on Tue Jun 01 2010 - 18:30:03 PDT
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