Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input

From: James Starlight <>
Date: Wed, 4 Mar 2015 15:48:34 +0100

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?


2015-03-04 15:10 GMT+01:00 James Starlight <>:
> Hi Bill,
> so I'd like to specify more:
> 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 <>:
>> You will need to strip all the water molecules out of the trajectories
>> using cpptraj prior to running 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 You can just use a
>> wild card or just list them all after the -y flag in the command.
>> I hope that helps.
>> -Bill
>> On Tue, Mar 3, 2015 at 6:58 AM, James Starlight <>
>> 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 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 as well as the stripped
>>> trajectory.
>>> I would be very thankful for any other solutions,
>>> James
>>> _______________________________________________
>>> AMBER mailing list
>> --
>> Bill Miller III
>> Post-doc
>> University of Richmond
>> 417-549-0952
>> _______________________________________________
>> AMBER mailing list

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Received on Wed Mar 04 2015 - 07:00:02 PST
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