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

From: James Starlight <>
Date: Wed, 4 Mar 2015 15:10:46 +0100

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?



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
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Received on Wed Mar 04 2015 - 06:30:05 PST
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