Just to conclude, never do the per res decomposition of MM-PBSA energy
without doing MM_GBSA energies with mm_pbsa.pl. The problem would be more
complicated than already mentioned.
On Tue, Sep 14, 2010 at 11:12 PM, manoj singh <mks.amber.gmail.com> wrote:
> Thanks for your reply at this time of the day :).
>
> I fund the source of the problem. In fact this is a bug when you do per
> residue decomposition of only PB energy and not of the GB energy.
>
> For those who might face this problem in future, make sure the header of
> *_com.all.out, *_rec.all.out, *_lig.all.out looks like this..
>
> --
> MM
> GB
> PB
> MS
> PB_SURFTEN 0.00542
> PB_SURFOFF 0.92
> GB_SURFTEN 0.0072
> GB_SURFOFF 0.00
> --
>
> The GB in second line would me missing if GB was set to 0 in mm_pbsa.pl,
> but for some reason, it is required to be present in these files.
>
> Thanks!
>
>
> On Tue, Sep 14, 2010 at 11:06 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Does it work if you only do one snapshot? Don't forget to remove the
>> files
>> that mm_pbsa.pl writes if you restart a simulation, since
>> mm_pbsa.pltypically appends to files, and you don't want it to append
>> to files that
>> begin with a failed calculation. This should help you pinpoint the
>> problem
>> -- it could be that the prmtop files are incompatible with the
>> trajectories,
>> certain residues were improperly specified, etc.
>>
>> Hope this helps,
>> Jason
>>
>> On Tue, Sep 14, 2010 at 10:55 PM, manoj singh <mks.amber.gmail.com>
>> wrote:
>>
>> > Thanks for the reply,
>> >
>> > Yes! I applied all bugfixes. This is Amber10.
>> >
>> > --
>> >
>> > On Tue, Sep 14, 2010 at 10:52 PM, Jason Swails <jason.swails.gmail.com
>> > >wrote:
>> >
>> > > Have you applied all bugfixes? What version of amber are you using?
>> > >
>> > > On Tue, Sep 14, 2010 at 9:59 PM, manoj singh <mks.amber.gmail.com>
>> > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > I am using mm_pbsa.pl to do per-residue decomposition. The
>> calculation
>> > > > appears to be trapped in a infinite loop with the following message.
>> I
>> > > have
>> > > > no clue what is going on and will be very thankful for any response.
>> > > >
>> > > > Manoj
>> > > >
>> > > > -----
>> > > >
>> > > > No values for GB_TGBSUR existing -> Skipping
>> > > > Processing PB SPBSOL
>> > > > Doing 1 PB SPB
>> > > > Doing 1 GB SGBSUR
>> > > > No values for GB_SGBSUR existing -> Skipping
>> > > > Processing PB TPBTOT
>> > > > Doing 1 PB TPBSOL
>> > > > No values for PB_TPBSOL existing -> Skipping
>> > > > Processing PB BPBTOT
>> > > > Doing 1 PB BPBSOL
>> > > > No values for PB_BPBSOL existing -> Skipping
>> > > > Processing PB BPBSOL
>> > > > Doing 1 PB BPB
>> > > > Doing 1 GB BGBSUR
>> > > > No values for GB_BGBSUR existing -> Skipping
>> > > > Processing PB SPBTOT
>> > > > Doing 1 PB SPBSOL
>> > > > No values for PB_SPBSOL existing -> Skipping
>> > > > Processing PB TPBSOL
>> > > > Doing 1 PB TPB
>> > > > Doing 1 GB TGBSUR
>> > > > No values for GB_TGBSUR existing -> Skipping
>> > > > Processing PB SPBSOL
>> > > > Doing 1 PB SPB
>> > > > Doing 1 GB SGBSUR
>> > > > No values for GB_SGBSUR existing -> Skipping
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Jason M. Swails
>> > > Quantum Theory Project,
>> > > University of Florida
>> > > Ph.D. Graduate Student
>> > > 352-392-4032
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Sep 20 2010 - 12:00:06 PDT
