<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
<title></title>
</head>
<body>
<p style="margin: 0px;">Hi all,</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">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?</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">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.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Does anyone have an idea what is happening?</p>
<br />
And if you do, can you please give a recommendation?<br />
<br />
Thank you,<br />
TJ Mustard<br />
mustardt@onid.orst.edu<br />
</body>
</html>