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
Received on Tue Jun 02 2009 - 01:15:05 PDT
