Re: [AMBER] problem with MMPBSA script

From: <Nadine.Homeyer.uni-duesseldorf.de>
Date: Thu, 01 Mar 2012 10:51:57 +0100

The execution of Sander for the calculation of MM, GB, or SAS was not
sucessful.
Set VERBOSE to 1 in the MM-PBSA input file and re-run the energy calculation.
Then have a look into the sander_com.1.out file for the error messages created
by Sander.
A description of this and other error messages can be found at
http://ambermd.org/Questions/mm_pbsa.html

Best regards,
Nadine


Zitat von kureeckal ramesh <kureeckalramesh.yahoo.co.in>:

>
>
> 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
>



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