[gmx-users] FEP energy errors with positional restraints?

Mark Abraham Mark.Abraham at anu.edu.au
Sun Feb 13 02:35:57 CET 2011

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.

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