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
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>>>>>> AMBER mailing list
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>>>
>>>
>>>
>>> --
>>> 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
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Received on Thu Mar 05 2015 - 05:00:02 PST
