Hi Bill,
just faced with the error of the post-processing of such trajectories
and topologiest
1) here I'm using ante-MMPBSA.py just to create three input topologies
for mmgbsa.py providing already stripped topology (only protein and
ligand).
ante-MMPBSA.py -p ${sim}/strip.protein.parm7 -c complex.prmtop -r
receptor.prmtop -l ligand.prmtop -n :MOL
2) then I use three generated prmtops (here I checked it according to
the number of atoms in each- all should be correct for first instance)
as well as 2 stripped trajectories as the inputs for the mmgbsa:
nmpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
mmgbsa_nm_${simulation}.dat -sp ${sim}/strip.protein.parm7 -cp
${sim}/strip.protein.parm7 -rp receptor.prmtop -y
${sim}/merged_md1_2.nc ${sim}/striped_md3.nc -lp ligand.prmtop >
progress.log 2>&1" > ./mmgbsa_${simulation}.pbs
3) having input file for the decomposition
&general
startframe= 1, interval=50, keep_files=2, netcdf=1
/
&gb
igb=5, saltcon=0.150,
/
&decomp
idecomp=1, csv_format=0, dec_verbose=0,
the calculation is begining- so there is no problems with any of
inputs- but occasionally I've obtained error
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13
CalcError: /home/cmoon/Prog/amber12/bin/cpptraj failed with prmtop
/home/cmoon/total_decomp/5p3_carvone/strip.protein.parm7!
Error occured on rank 14.
How it could be fixed most trivially?
James
2015-03-05 13:44 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
> Personally, I use tleap to generate all prmtops necessary for MMPBSA.py calculations prior to running any simulation. But if you have already started running simulations, I would advise using ante-MMPBSA.py
>
> -Bill
>
> On Mar 5, 2015, at 6:39 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>
>> so in simplest case only 2 inputs should be provided : stripped
>> merged trajectory as well as stripped topology for each system
>> shouldn't it? BTW is it possible to use ante-mmpbsa to strip common
>> mask from several input trajectories consisted of different number of
>> solvent (so its number of atoms will be also different) or it will
>> better anyway to use tleap?
>>
>> James
>>
>> 2015-03-05 11:45 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
>>> Thanks alot!
>>>
>>> James
>>>
>>> 2015-03-04 16:38 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
>>>> For MMPBSA.py calculations, explicit solvent molecules are never used for
>>>> the calculation. MMPBSA.py removes the solvent before doing any
>>>> calculations. So if you give it a trajectory (or multiple trajectories)
>>>> without water molecules along with a dry/stripped topology, the calculation
>>>> will be the same, but MMPBSA.py just won't have to remove the water atoms
>>>> first.
>>>>
>>>> In this case, you do not need to specify anything for the strip mask. If
>>>> you don't give MMPBSA.py a solvated topology file, it knows not to strip
>>>> any residues from the trajectory.
>>>>
>>>> You can use the startframe variable in the &general namelist to specify
>>>> what frame you want the calculation to start on. And I believe that is for
>>>> each trajectory if you provide more than one.
>>>>
>>>> -Bill
>>>>
>>>> On Wed, Mar 4, 2015 at 9:48 AM, James Starlight <jmsstarlight.gmail.com>
>>>> wrote:
>>>>
>>>>> and some additional questions:
>>>>>
>>>>> 1- what should be provided in the mmgbsa.input file for the stripped
>>>>> mask in case when I use already stripped from the solvent trajectories
>>>>> 2- how it possible not to take into the analysis x fist snapshots from
>>>>> each processed trajectory used within one mmgbsa calculation?
>>>>>
>>>>> James
>>>>>
>>>>> 2015-03-04 15:10 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
>>>>>> Hi Bill,
>>>>>>
>>>>>> so I'd like to specify more:
>>>>>> mmgbsa.py accept *several* input trajectories files (specified after
>>>>>> its -y flag) each of which should consist only of the atoms for ligand
>>>>>> and receptor as well as stripped topology with the same atoms isn't
>>>>>> it? so for calculation of the free energy of binding and its
>>>>>> decomposition the presence of solvent within the system is not needed?
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> James
>>>>>>
>>>>>> 2015-03-03 16:23 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
>>>>>>> You will need to strip all the water molecules out of the trajectories
>>>>>>> using cpptraj prior to running MMPBSA.py since they all have different
>>>>>>> numbers of water molecules, and then use the dry prmtop and just don't
>>>>>>> provide a solvated prmtop. You don't have to merge them all into one
>>>>>>> trajectory using cpptraj prior to running MMPBSA.py. You can just use a
>>>>>>> wild card or just list them all after the -y flag in the MMPBSA.py
>>>>> command.
>>>>>>>
>>>>>>> I hope that helps.
>>>>>>>
>>>>>>> -Bill
>>>>>>>
>>>>>>> On Tue, Mar 3, 2015 at 6:58 AM, James Starlight <jmsstarlight.gmail.com
>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear Amber users!
>>>>>>>>
>>>>>>>> I'm going to perform per-residue decomposition analysis for several
>>>>>>>> protein-ligand systems having 3 independent trajectories for each
>>>>>>>> system. I wounded to know
>>>>>>>> 1) is it possible to include several trajectories tax the standard
>>>>>>>> input to MMPBSA.py or alternatively I should to merge all trajectories
>>>>>>>> for the same system together using cpptraj?
>>>>>>>> 2) what I should do if some of the trajectories for the same system
>>>>>>>> are consisted of different number of atoms (and its parm7 files also
>>>>>>>> differs)-> because each time each system has been solvated de novo->
>>>>>>>> so the number of solvent molecules in identical protein-ligand systems
>>>>>>>> are differs. In these regards Is it possible to i) strip all solvent
>>>>>>>> using cpptraj from each trajectory and ii) to join all of them
>>>>>>>> together ( consisted of only protein-ligand atoms) iii) to provide
>>>>>>>> stripped parm7 file for the MMPBSA.py as well as the stripped
>>>>>>>> trajectory.
>>>>>>>>
>>>>>>>> I would be very thankful for any other solutions,
>>>>>>>>
>>>>>>>> James
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Bill Miller III
>>>>>>> Post-doc
>>>>>>> University of Richmond
>>>>>>> 417-549-0952
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
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>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
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>>>>
>>>>
>>>>
>>>> --
>>>> Bill Miller III
>>>> Post-doc
>>>> University of Richmond
>>>> 417-549-0952
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Received on Mon Mar 16 2015 - 06:30:02 PDT
