Re: [AMBER] MMPBSA problem binding energy calculation

From: Bill Miller III <brmilleriii.gmail.com>
Date: Tue, 1 Jun 2010 07:02:09 -0400

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
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Received on Tue Jun 01 2010 - 04:30:05 PDT
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