Unify alternate location handling and LES capabilities

[swails]

LES (locally enhanced sampling) deals with replicating parts of the system N times and simulating all of them (with the total interaction being an average of all copies). These copies don't interact with each other, but each interact with their surroundings.

There are known deficiencies here, as the copies do interact with each other through, for example, explicit solvent (since water interacts with every copy). However, many proteins have atoms that have "alternate conformations" in crystal structures, and LES maps onto this problem fairly well conceptually. The goal here is to add the necessary functionality in ParmEd to handle Amber LES prmtops and coordinate files with the existing alternate location functionality in ParmEd.

In particular:

• [ ] Figure out how addles and LES work in Amber in general
• [ ] Add capability for AmberParm to parse LES-capable prmtops and restarts
• [ ] Map LES functionality with Atom.other_locations so it interoperates with altlocs in PDB files

Possibly also

• [ ] Implement addles in ParmEd

[hainm]

Jason,

is there any (if existing) progress on this? I am in Phenix meeting now and am interested to use ParmEd for LES protein refinement. (too lazy to learn others :D). Phenix has very broad users so ParmEd can have broader impact.

[swails]

No progress yet :). I never learned LES well enough.

[hainm]

I never learned LES well enough.

me neither. :D