I am writing you in a hope that the following problems will be resolved with your help.
I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.
Treating with waters as a chain is too exhausting for laptop calculating abilities and, consequently, the process is killed.
The situation, when WAT residues are replaced with HOH residues is more feasible solution for calculating capacities. But it ends up with an error "Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose." in 'replace' mode for ExplicitWater mover. It is confused by jump renumbering.
And, anyway, treating with water environment as a chain sounds like a nonsense.
So, I returned to WAT instead of HOH. As I told before, in order to make the calculation feasible for hardware capacities, I decided to break water chain into separate residues with a flag -in:file:treat_residues_in_these_chains_as_separate_chemical_entities "W". Nevertheless, the chain_util.cc started to create individual chain ID for every water residue. Since there are several hundreds of them, the set of chars and digits are fastly run out and entire calculation finishes with an error
[ ERROR ] UtilityExitException
ERROR: too many chains to map to letters!!!
After that I commented out the mentioned flag and inserted TER after every water residue.
Would anyone here be kind to tell me, how to keep all the same chain id for all water residues? The last thing which I did - commenting out the #include <core/pose/chains_util.hh> statement in ExplicitWaterMover.cc script. But it also didn't solve the problem.
Or probable it would be better to use single HOH residues instead WAT ones, since the calculation with them is not so time- and computational-resources-consuming?
Last, but not the least question - why the water positioning is so exhausting within CM app in terms of calculating? At least, it seems as if the AAs side-chain packing looks as more complicated task than handling with little water molecules.
I attach res, flag and XML-protocol files for better clarity.
I will be sincerely grateful for your response and I am looking forward to it.