Dear Nadine
Thank you for the reply. I saw the sander_com.1.out file and the error message is as follows
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
FATAL: NATOM mismatch in coord and topology files
-------------------------------------------------------------------------------------------------------------
Please suggest some solution
Regards
Ramesh K V
________________________________
From: "Nadine.Homeyer.uni-duesseldorf.de" <Nadine.Homeyer.uni-duesseldorf.de>
To: kureeckal ramesh <kureeckalramesh.yahoo.co.in>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 1 March 2012 3:21 PM
Subject: Re: [AMBER] problem with MMPBSA script
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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Received on Thu Mar 01 2012 - 03:00:02 PST
