what I found on the bottom
FATAL: NATOM mismatch in coord and topology files
I've checked all topologies and it seems ok for me
n atoms of complex.prmtop = n atoms of receptor.prmtop + n atoms of
ligand.prmtop
it;s strange because I don't see here where the coordinate file (smth
like protein.inpcrd) are provided in the below mmgbsa input
mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
mmgbsa_nm_OR5P3_quinoline.dat -sp
/home/cmoon/argh/OR5P3_quinoline/protein.parm7 -cp
/home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/complex.prmtop
-rp /home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/receptor.prmtop
-y /home/cmoon/argh/OR5P3_quinoline/md3.nc -lp
/home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/ligand.prmtop
> progress.log 2>&1
2015-04-02 16:50 GMT+02:00 Kenneth Huang <kennethneltharion.gmail.com>:
> James,
>
> Generally speaking, you can always make the stripped topologies you need in
> tleap, usually before you add ions and solvent, or you could just reload
> your starting structure into tleap and save it without solvent/ions. That
> said, ante-MMPBSA is good for when you don't have your starting structure
> anymore, or don't want to backtrack, or don't know what masks you want to
> use.
>
> As for your error, try checking the MMPBSA gb mdout file- it should give
> you a more descriptive error message.
>
> Best,
>
> Kenneth
>
> On Thursday, April 2, 2015, James Starlight <jmsstarlight.gmail.com
> <javascript:_e(%7B%7D,'cvml','jmsstarlight.gmail.com');>> wrote:
>
>> Dear Friends!
>>
>> I've faced with the problem during mmgbsa analysis of my system:
>>
>>
>>
>> Firstly I have no problems with processing of initial protein.parm7
>> obtained using
>>
>> ante-MMPBSA.py -p ${sim}/protein.parm7 -c
>> ${sim}/decomposition_${simulation}/complex.prmtop -r
>> ${sim}/decomposition_${simulation}/receptor.prmtop -l
>> ${sim}/decomposition_${simulation}/ligand.prmtop -s
>> :WAT:Cl-:NA+:K+:PPC -n :MOL
>>
>> Stripping :WAT:Cl-:NA+:K+:PPC (solvent) from original topology, output
>> is
>> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
>> Done stripping solvent!
>>
>> Creating receptor topology file by stripping :MOL from
>>
>> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
>> Done creating receptor topology file!
>>
>> Creating ligand topology file by stripping !(:MOL) from
>>
>> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
>> Done creating ligand topology file!
>>
>>
>>
>> but then during decomposition using mmgbsa.py I've obtained error at
>> the begining of calculations:
>> (here the input file consisted of paths because it was produced by my
>> bash script)
>> mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
>> mmgbsa_nm_OR5P3_androstenone.dat -sp
>> /home/cmoon/total_decomp/OR5P3_androstenone/protein.parm7 -cp
>> complex.prmtop -rp receptor.prmtop -y
>> /home/cmoon/total_decomp/OR5P3_androstenone/md1.nc
>> /home/cmoon/total_decomp/OR5P3_androstenone/md2.nc
>> /home/cmoon/total_decomp/OR5P3_androstenone/md3.nc -lp ligand.prmtop >
>> progress.log 2>&1
>>
>> ::
>> Running calculations on normal system...
>>
>> Beginning GB calculations with /home/cmoon/Prog/amber12/bin/sander
>> calculating complex contribution...
>> CalcError: /home/cmoon/Prog/amber12/bin/sander failed with prmtop
>> complex.prmtop!
>> Error occured on rank 3.
>> Exiting. All files have been retained.
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
>> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
>>
>> I've checked all prmtop files used here but have not found any errors
>> here (the atom numbers and its composition is correct in all 3
>> topologies made by ante-mmbsa). Could someone suggest me some
>> resolution if the issue and alternative method to made stripped
>> topologies avoiding ante-mmbsa?
>>
>> Thanks!!
>>
>> James
>>
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>>
>
>
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> here could not dream of heaven?
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Received on Thu Apr 02 2015 - 08:30:02 PDT
