[AMBER] Error with MM-PBSA perl file for pairwise residue decomposition

From: Monika Sharma <mondyn.gmail.com>
Date: Fri, 25 Mar 2011 08:39:16 +0530

Dear All,
I am trying to do pairwise residue-decomposition using mm_pbsa.pl file. I am
using AMBER10 software. The problem occurs during the statistics part. I
tried to search the mailing list. A similar post I saw too, but with no
reply.

 I have used the input file as

.GENERAL
PREFIX snap
PATH ./snaps
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT complex.top
RECPT receptor.top
LIGPT ligand.top
#
GC 0
AS 0
DC 1
MM 1
GB 1
PB 0
MS 0
#
NM 0
.DECOMP
DCTYPE 4
#
COMREC 1-71
COMLIG 72-72
COMPRI 1-71 72-72
RECRES 1-71
RECPRI 1-71
RECMAP 1-71
LIGRES 1-1
LIGPRI 1-1
LIGMAP 72-72
.MM
DIELC 1.0
.GB
IGB 2
GBSA 2
SALTCON 0.0005
EXTDIEL 78.3
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00

PBSA run went file and it created 3 heavy files for complex, receptor and
ligand, totaling to about 4 GB. There is no error reported while calculation
of values for each snapshot.
This is an excerpt of complex output file

MM
GB
MS
GB_SURFTEN 0.0072
GB_SURFOFF 0.00
1
TDC 1-> 1 0.000 -3.166 58.463 -29.560 840.348
TDC 1-> 2 0.000 -3.551 -16.884 -9.707 -378.577
TDC 1-> 3 0.000 -0.292 6.277 -6.186 0.000
TDC 1-> 4 0.000 -0.029 3.703 -3.659 0.000
TDC 1-> 5 0.000 -0.008 2.652 -2.622 0.000
TDC 1-> 6 0.000 -0.003 2.038 -2.015 0.000
TDC 1-> 7 0.000 -0.002 1.793 -1.773 0.000
TDC 1-> 8 0.000 -0.001 1.707 -1.689 0.000
TDC 1-> 9 0.000 -0.001 1.648 -1.631 0.000
TDC 1-> 10 0.000 -0.000 1.601 -1.584 0.000
TDC 1-> 11 0.000 -0.000 1.663 -1.645 0.000
TDC 1-> 12 0.000 -0.000 1.715 -1.696 0.000
TDC 1-> 13 0.000 -0.000 1.465 -1.449 0.000
TDC 1-> 14 0.000 -0.000 1.244 -1.231 0.000
TDC 1-> 15 0.000 -0.000 1.106 -1.095 0.000
TDC 1-> 16 0.000 -0.000 1.068 -1.058 0.000
TDC 1-> 17 0.000 -0.000 1.001 -0.991 0.000
TDC 1-> 18 0.000 -0.000 0.971 -0.961 0.000
TDC 1-> 19 0.000 -0.000 0.969 -0.960 0.000
TDC 1-> 20 0.000 -0.000 0.955 -0.946 0.000
TDC 1-> 21 0.000 -0.000 0.960 -0.950 0.000
.......................................................................................................
.......................................................................................................
TDC 1-> 69 0.000 -0.118 1.549 -1.546 -3.437
TDC 1-> 70 0.000 -0.430 2.353 -2.743 -39.767
TDC 1-> 71 0.000 0.488 -10.212 1.657 -161.388
TDC 1-> 72 0.000 -0.000 -0.031 0.030 0.000
TDC 2-> 1 0.000 -3.551 -16.884 -9.707 -338.524
TDC 2-> 2 0.000 -4.994 18.538 -78.942 1369.696
TDC 2-> 3 0.000 -6.268 3.342 -28.524 -503.818
TDC 2-> 4 0.000 -0.263 17.073 -16.884 0.000
TDC 2-> 5 0.000 -0.031 11.360 -11.225 0.000
-------------------------------------------------------------------------------
and so on.........

I am not able to understand why the first column is 0 (it is 0.000 for each
snapshot of complex, receptor or ligand) and what is meant by that?

The problem occurs while doing the statistics. It seems the program ends
without error while reading the output files for complex.

.................................................................................
    Calc contrib for ./snaps/snap_lig.crd.1999
        Calc MM/GB/SAS
    Calc contrib for ./snaps/snap_lig.crd.2000
        Calc MM/GB/SAS

=>> Doing statistics
=>> Reading input
=>> Reordering files
    Final order:
    1. snap_com.all.out: 1 - 71 72 - 72
    2. snap_rec.all.out: 1 - 71
    3. snap_lig.all.out: 72 - 72
=>> Reading files
    Reading snap_com.all.out

At this point the program exits without error. By this, I mean I cannot see
any pbsa command running on the machine using ps -A or top. I tried
re-running the program twice for whole calculation itself, but with no use.

Please advise how to get out of this problem. I have patched the recent
bugfixes for Amber10.

Thanks in advance.
Regards
Monika


-- 
((`_.[Monika]._))
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Received on Thu Mar 24 2011 - 20:30:03 PDT
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