Restarting protein system simulation using different ligand

From: Kevin Kastner (
Date: Thu Oct 13 2011 - 12:22:41 CDT

I have been running an explicit solvent simulation in NAMD 2.8 containing a
transmembrane protein, ligand, lipid membrane, water, and ions. I generated
the system, excluding the ligand, using the NAMD membrane tutorial. I then
add the ligand in and then convert it for use with the Amber force field. I
run the three preparatory simulations, then however many full simulations I

What I want to do is replace the ligand that is in the system at the end of
the simulation with another one and continue the simulation. (I tried this
before but it complained that I had exceeded the periodic cell boundary.) Is
it possible to do this without having to remake the entire system from
scratch? I doubt that I can use the .coor and .vel restart files as some
atoms have been replaced, but would it be possible to use either the .xsc or
.xst files, or is there a better way? Oh, and the ligand is contained within
the protein, so (hopefully) it should not exceed the periodic cell boundary--0015174c0ebe59978f04af316340--

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