[AMBER] problem with MMPBSA script

From: kureeckal ramesh <kureeckalramesh.yahoo.co.in>
Date: Thu, 1 Mar 2012 14:22:39 +0530 (IST)

Dear AMBER users

1) I have completed 10ns os MD simulation for one of my protein solvated with water (no drug interaction).

2) Now I am interested in free energy calculation for which which I followed the extracts_coords.mmpbsa  and binding_energy.mmpbsa  as recommeded in the tuotrial for amber (http://ambermd.org/tutorials/advanced/tutorial3/section3.htm)
3) Since I am working with only protein solvated with water, the above 2 scripts were changed accordingly and is shown below.

4) Though extracts_coords.mmpbsa was  generate the several snapshot files, I was not able to succedd with bindign_energy calcaulation using binding_energy.mmpbsa script  AS THE  OUTPUT showed error


SCRIPT DETAILS

I . extracts_coords.mmpbsa
--------------------------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------------------------
PREFIX                snapshot
PATH                  ./
#
COMPLEX               1
RECEPTOR              0
LIGAND                0

COMPT                 ./2NPD_solvated.prmtop
#RECPT                 ./2NPD.prmtop

#
GC                    1
AS                    0
DC                    0
#
MM                    0
GB                    0
PB                    0
MS                    0
#
NM                    0
#
################################################################################
.MAKECRD
#   
BOX                   YES
NTOTAL                42193
NSTART                1
NSTOP                 200
NFREQ                 1
#
NUMBER_LIG_GROUPS     0
#LSTART                2622
#LSTOP                 3862
NUMBER_REC_GROUPS     1
RSTART                1
RSTOP                 2621
#
#################################################################################
.TRAJECTORY
#
TRAJECTORY            ./prod1.mdcrd
TRAJECTORY            ./prod2.mdcrd
TRAJECTORY            ./prod3.mdcrd
TRAJECTORY            ./prod4.mdcrd
TRAJECTORY            ./prod5.mdcrd
TRAJECTORY            ./prod6.mdcrd
TRAJECTORY            ./prod7.mdcrd
TRAJECTORY            ./prod8.mdcrd
TRAJECTORY            ./prod9.mdcrd
TRAJECTORY            ./prod10.mdcrd
TRAJECTORY            ./prod11.mdcrd
TRAJECTORY            ./prod12.mdcrd
TRAJECTORY            ./prod13.mdcrd
TRAJECTORY            ./prod14.mdcrd
TRAJECTORY            ./prod15.mdcrd
TRAJECTORY            ./prod16.mdcrd
TRAJECTORY            ./prod17.mdcrd
TRAJECTORY            ./prod18.mdcrd
TRAJECTORY            ./prod19.mdcrd
TRAJECTORY            ./prod20.mdcrd
-----------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------


II. binding_energy.mmpbsa
----------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------#
PREFIX                snapshot
PATH                  ./
#
COMPLEX               1
RECEPTOR              1
LIGAND                0
#
COMPT                 ./2NPD_solvated.prmtop
RECPT                 ./2NPD.prmtop

#
GC                    0
AS                    0
DC                    0
#
MM                    1
GB                    1
PB                    1
MS                    1
#
NM                    0
#
################################################################################
.PB
#
PROC                  2
REFE                  0
INDI                  1.0
EXDI                  80.0
SCALE                 2
LINIT                 1000
PRBRAD                1.4
ISTRNG                0.0
RADIOPT               0
NPOPT                 1
CAVITY_SURFTEN        0.0072
CAVITY_OFFSET         0.00
#
SURFTEN               0.0072
SURFOFF               0.00
#
################################################################################
.MM
#
DIELC                 1.0
#
################################################################################
.GB
#
IGB                   2
GBSA                  1
SALTCON               0.00
EXTDIEL               80.0
INTDIEL               1.0
#
SURFTEN               0.0072
SURFOFF               0.00
#
################################################################################
.MS
#
PROBE                 0.0
#
----------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------
error after running binding energycommand
ramesh.sgiUV:~> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
        /data1/apps/amber/10/intel-mkl-openmpi/exe/sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p ./2NPD_solvated.prmtop not successful


details of the binding_energy.log file
--------------------------------------------------

=>> Init data
    Presuming executables of amber suite to be in /data1/apps/amber/10/intel-mkl-openmpi/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH => ./
    Found COMPLEX => 1
    Found RECEPTOR => 0
    Found LIGAND => 0
    Found COMPT => ./2NPD_solvated.prmtop
    Found RECPT => ./2NPD.prmtop
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 1
    Found PB => 1
    Found MS => 1
    Found NM => 0
    Found PROC => 2
    Found REFE => 0
    Found INDI => 1.0
    Found EXDI => 80.0
    Found SCALE => 2
    Found LINIT => 1000
    Found PRBRAD => 1.4
    Found ISTRNG => 0.0
    Found RADIOPT => 0
    Found NPOPT => 1
    Found CAVITY_SURFTEN => 0.0072
    Found CAVITY_OFFSET => 0.00
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 1
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found PROBE => 0.0

=>> Checking sanity
    Checking GENERAL
    Setting START to default 1
    Setting STOP to default 10e10
    Setting OFFSET to default 1
    Setting VERBOSE to default 0
    Checking MM
    Checking PB
    Checking GB
    Checking MS

=>> Creating input
    Sander input
    PBSA input

=>> Calculating energy / entropy contributions
    Calc contrib for ./snapshot_com.crd.1
        Calc MM/GB/SAS
----------------------------------------------------------------------


Resquest you to kindly suggest where I should make corrections in the script to calculate the binding free energy between the protein and the water ONLY


Thanking you
Ramesh K V
Dept of Biotech
Jain University Bangalore







________________________________
 From: kureeckal ramesh <kureeckalramesh.yahoo.co.in>
To: "amber.ambermd.org" <amber.ambermd.org>
Cc: "sudhadeshmukh.yahoo.com" <sudhadeshmukh.yahoo.com>
Sent: Thursday, 1 December 2011 10:44 AM
Subject:
 

Dear amber user

As a part of sustival tutorial (MD simulation of protein-drug interaction), I was able to generate sustiva.mol2 file.
Got an error while proceeding further (i. e, after executing tleap command) which is as follows

---------------------------------------------------------------------
> SUS = loadmol2 sustiva.mol2
Loading Mol2 file: ./sustiva.mol2
Reading MOLECULE named SUS
/data1/apps/amber/10/intel-mkl-openmpi/exe/tleap: line 8: 25824 Segmentation fault      /data1/apps/amber/10/intel-mkl-openmpi/bin/teLeap -I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/prep -I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/lib -I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/parm -I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/cmd
 $*
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------

looking forward for your help

With regards
Ramesh K V
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Received on Thu Mar 01 2012 - 01:00:02 PST
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