As the error message suggest, your topology and coordinate files contain
different numbers of atoms. Form the name of your topology file I suppose that
it contains water molecules. For implicit solvent calculations topologies of
un-solvated systems should be used, as demonstrated in the tutorial.
Best regards,
Nadine
Zitat von kureeckal ramesh <kureeckalramesh.yahoo.co.in>:
> 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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