Okay, so the error here isn't with your topologies- those are fine. It's
that your topologies and coordinate files aren't matching up for some
reason. Assuming that they're the ones that you ran MD with, my best guess
is that there's something leftover that you forgot to strip out when you
ran ante-MMPBSA?
You can also try making a pdb file with ambpdb using the same inputs, or
loading your trajectory with the relative topology into VMD to see if it
works. If both of them fail, then something is missing from your topologies
that's still in your trajectory.
Best,
Kenneth
On Thu, Apr 2, 2015 at 11:08 AM, James Starlight <jmsstarlight.gmail.com>
wrote:
> 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> > Ask yourselves, all of you, what power would hell have if those
> imprisoned
> > here could not dream of heaven?
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 02 2015 - 09:00:04 PDT
