Hi Jas,
I have done this in the past. It is quite cumbersome since it requires
many steps, so not sure if there is a more elegant "built in" method to
do so.
The way I have done it is as follows:
1. divide your molecule in residues where each residue corresponds to an
atom
2. re-build the parameter files, but make sure that the order of atoms
remains the same. Check that you can open the previous trajectory with
the new parameter file.
3. carry out the energy decomposition analysis, you will get the output
for each residue which now corresponds to each atom
Hope this helps!
Bruno
On 27/02/17 13:52, Jas Kalayan wrote:
> Dear Amber members,
>
> Is it possible to determine just the MM part of the MMPBSA calculation of free energy? I wanted to determine only the MM energy contribution of each atom of a molecule in a vacuum using Amber 14.
>
> >From per-residue decomposition, I can see that the .mdout.0 files break down energies of each side-chain and backbone for each frame into internal, vdw, eel, pol and sas. But I would have thought the internal, vdw and eel energies per residue were determined from the sum of all atoms in the residue. Would this also be the case for all atoms in the molecule summed to give the energy of the whole molecule? If so would it be possible to effectively go back a step and extract internal, vdw and eel energies for each atom?
>
> Kind Regards,
>
> Jas
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Received on Wed Mar 01 2017 - 07:00:03 PST
