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
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
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>
>
>
> --
> Bill Miller III
> Post-doc
> University of Richmond
> 417-549-0952
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Mar 05 2015 - 03:00:03 PST
