Re: [AMBER] MMPBSA problem binding energy calculation

From: Bill Miller III <brmilleriii.gmail.com>
Date: Tue, 1 Jun 2010 21:18:39 -0400

What exactly do you mean you "can not see anything in VMD"? I'm guessing
that it doesn't look like it is supposed to. As Jason mentioned, this means
that there is almost certainly a mismatch between your prmtop and coordinate
files that you generated. Thus, something has gone wrong with the generating
coordinates step, and you should not proceed to the binding energy
calculation until you can successfully visualize the generated coordinate
files with the correct prmtops. You should check very carefully over the
prmtop files to make sure they match the atom number definitions you are
supplying mm_pbsa.pl in the input file (extract_coords.mmpbsa).
Specifically, make sure that the receptor and complex prmtops each have the
3 Zn ions that you are specifying in the atom definitions. Keeping ions
during an MM/PBSA calculation can be a very tricky process in itself.

I hope this helps.

Good luck!

-Bill

On Tue, Jun 1, 2010 at 9:05 PM, 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
> _______________________________________________
> 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
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Received on Tue Jun 01 2010 - 18:30:05 PDT
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