AMBER Archive (2009)

Subject: Re: [AMBER] MMPBSA and mm_pbsa_statistics.pl error

• Previous message: Workalemhu Berhanu: "[AMBER] preparation of two solutes of organic molecules in a simulation box"
• In reply to: john smith: "[AMBER] MMPBSA and mm_pbsa_statistics.pl error"
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John,

Maybe you can show us your three files "snapshot_com.all.out",
"snapshot_rec.all.out", "snapshot_lig.all.out"?

All the best,
Ray

john smith wrote:
> Dear All,
>
> I am facing a problem for the calculating MMPBSA/GBSA energy for
> protein-ligand complex for a single trajectory version. I have
> followed the
> procedure almost similar to that given in the tutorial for MMPBSA at the
> AMBER's site.
>
> I ran the script for mm_pbsa.pl with binding_energy.mmpbsa which
> terminated
> with an error:
> "=>> Calc delta from raw data
> No data for 0+1 MM BOND 50"
>
>
> But the calculation had generated 3 files namely snapshot_com.all.out,
> snapshot_rec.all.out, snapshot_lig.all.out. Hence I tried to run the
> mm_pbsa_statistics.pl script manually with following commands and the
> corresponding output is given below.
>
> 1. *command:* # mm_pbsa_statistics.pl 1 0
> snapshot_statistics.insnapshot_statistics_m12.out 1 50
> *output at the end:*
> "=>> Calc delta from raw data
> No data for 0+1 MM BOND 50"
> 2. *command:* # mm_pbsa_statistics.pl 2 0
> snapshot_statistics.insnapshot_statistics_m12.out 1 50
> *output at the end*
> "=>> Print output (snap) to snapshot_statistics.out.snap
> That operation doesn't make sense with calc_delta == 2"
>
>
> When I set calc_delta = 1, the calculation ends with the above error, and
> produces snapshot_statistics.out file with all the parameters for
> complex,
> receptor & ligand, but no delta terms.
>
> When I set calc_delta = 2, the calculation ends with the mesage shown
> above,
> and produces snapshot_statistics.out file similar to that given in tht
> tutorial for MMPBSA. However, the internal energy term INT is not zero,
> which as per the tutorial should be zero for a single trajectory version.
>
> The same problem occurs for another ligand which is a positional
> isomer of
> the original ligand.
>
> Is everything going fine with the calculation or I have done something
> wrong
> with the later part of the calculation?
> I am attaching the output file (*snapshot_statistics_m12.out*) for the
> command 2.
> Thanks in advance
>
> -Regard
> John

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• Previous message: Workalemhu Berhanu: "[AMBER] preparation of two solutes of organic molecules in a simulation box"
• In reply to: john smith: "[AMBER] MMPBSA and mm_pbsa_statistics.pl error"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]