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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 01 2012 - 01:00:02 PST
