On 13/02/2011 11:49 AM, TJ Mustard wrote:
Hi all,
I have been testing the ability of taking a sphere of a protein around
a ligand, and positionally restrain the specified alpha carbons. I was
hoping to keep non connected protein chains from drifting apart. I
have been able to run these md/fep jobs, but I get huge interaction
energies for the ligand, which has no positional restraints on it. I
also don't restrain any atoms within the rvdw, rcoulomb and rlist
radii. Am I thinking this is a possibility when it is physically
impossible to simulate?
I doubt it.
Currently I am selecting all residues around the ligand that have an
atom within 20 Angstroms. I then save this as a pdb file and then run
it through pdb2gmx, manually create a posres.itp file for each "chain"
with their first and last residue's alpha carbon. Once I turn off
these positional restraints the FEP energies drop down to "normal" levels.
Does anyone have an idea what is happening?
And if you do, can you please give a recommendation?
I'd guess you're not restraining how you think you are :-) Bear in mind
that position restraints are indexed relative to a [moleculetype] (and
must be #included there), and not the whole system.
The combination of g_select and genrestr is probably a more reliable and
documentable way to generate your position restraints.
Mark
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