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
Received on Thu Apr 02 2015 - 08:00:04 PDT
