AMBER Archive (2009)

Subject: [AMBER] MMPBSA and mm_pbsa_statistics.pl error

From: john smith (johnsmithgr8_at_gmail.com)
Date: Tue Jun 02 2009 - 00:38:54 CDT

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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