Hi,
Could you include your input file for the calculation? This one looks ok for
snapshot generation.
Also there should be an error in the .out file for that ligand:
pbsa_lig.1.out
Does tailing any of the pl_*.all.out give errors? where * can be com, rec
or lig.
When you say failed did it give an error to the screen or just hang?
Try just a GB calculation by itself, if that works include PB then decomp.
I've been having similar problems =)
Oliver
On 26 September 2010 15:45, juzer stationwala <juzer.niper.gmail.com> wrote:
> hello all
> I have been facing the problem with the binding free energy calculation
> with MMPBSA
> while using the following script I was able to successfully carry out
> binding free energy for two snapshot
> however when I tried to perform the analysis for larger number of snapshot
> the process died while carrying calculation of snapshot pertaining to
> ligand
>
> Initially I tried to perform calculation by taking 2 snapshot starting from
> 1 upto 2
> It worked well but failed when the 21 snapshots were taken for which the
> the
> range selected was from 400-420 but it failed.
>
> I am using amber 10
> *
> **my extract_coords.mmpbsa*
>
> PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./gsk-ref.prmtop
> RECPT ./gsk-nn.prmtop
> LIGPT ./lig.prmtop
> #
> GC 1
> AS 0
> DC 0
> #
> MM 0
> GB 0
> PB 0
> MS 0
> #
> NM 0
> BOX YES
> NTOTAL 55388
> NSTART 400
> NSTOP 420
> NFREQ 1
> #
> NUMBER_LIG_GROUPS 1
> LSTART 5669
> LSTOP 5702
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 5668
> TRAJECTORY ./prod.mdcrd
> *
> last few lines from my binding_energy.log file *
> Calc contrib for ./snapshot_rec.crd.20
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
> Generate PQR
> Calc MS
> Calc contrib for ./snapshot_rec.crd.21
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
> Generate PQR
> Calc MS
> Calc contrib for ./snapshot_lig.crd.1
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
>
> any help would be highly obliged
> --
> Regards:
>
> Juzer Stationwala,
> Center for Pharmacoinformatics,
> National Institute of Pharmaceutical Education & Research
> (NIPER)
> Mohali,
> Punjab.
> India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Sep 26 2010 - 09:00:04 PDT
