[AMBER] Query regarding mmpbsa run

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Mon, 14 Mar 2011 16:29:38 +0530

Hi All,
I am trying to calculate the binding free energy for my protein ligand
complex using mmpbsa.pl script. In the log file I am getting following
error.
 Reading snapshot_com.all.out
    WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
    WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
    WARNING: Missing EPB for PB in 0 -> Taken from -1
    WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0
    WARNING: Missing ELRAELE for PB in 1 -> Taken from 0
    WARNING: Missing EPB for PB in 1 -> Taken from 0
    WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1
    WARNING: Missing ELRAELE for PB in 2 -> Taken from 1
    WARNING: Missing EPB for PB in 2 -> Taken from 1
    WARNING: Missing PBNONPOL for PB in 3 -> Taken from 2
    WARNING: Missing ELRAELE for PB in 3 -> Taken from 2
    WARNING: Missing EPB for PB in 3 -> Taken from 2
    WARNING: Missing PBNONPOL for PB in 4 -> Taken from 3
    WARNING: Missing ELRAELE for PB in 4 -> Taken from 3
    WARNING: Missing EPB for PB in 4 -> Taken from 3
    WARNING: Missing PBNONPOL for PB in 5 -> Taken from 4
    WARNING: Missing ELRAELE for PB in 5 -> Taken from 4
    WARNING: Missing EPB for PB in 5 -> Taken from 4
    WARNING: Missing PBNONPOL for PB in 6 -> Taken from 5
    WARNING: Missing ELRAELE for PB in 6 -> Taken from 5
    WARNING: Missing EPB for PB in 6 -> Taken from 5
    WARNING: Missing PBNONPOL for PB in 7 -> Taken from 6

I googled the term and found that I need to modify the *
mm_pbsa_statistics.pm*. But I cant modify the same as I cant access
superuser. I wanted to ask whether I can ignore the following warning or It
affects the output energy.
Another query is regarding
snapshot_statistics.out<http://ambermd.org/tutorials/advanced/tutorial3/files/snapshot_statistics.out>.
I am not getting this file. I am *.all.out files for receptor, ligand and
for complex. There is no error in the .out files. But still I am not getting
the snapshot_statistics.out<http://ambermd.org/tutorials/advanced/tutorial3/files/snapshot_statistics.out>
.

Please suggest me where I am wrong.

Thanks and Regards,
Hirdesh


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Received on Mon Mar 14 2011 - 04:30:03 PDT
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