Re: [AMBER] Cluster restraints

From: David A Case <>
Date: Tue, 28 Jul 2015 20:49:47 -0400

On Tue, Jul 28, 2015, Damiano Spadoni wrote:
> I am working on a quite big tetrameric protein made up by four chains
> (of course). Every monomer contains one Fe4-S4 cluster. I want
> to define in my MD production step, distance restraints on all the
> clusters.

Questions: (1) what force field parameters are you using for the Fe4S4
clusters? [We have some FS4 parameter files that I should probably try to
the contributed parameters database, but I haven't had the time to do it.]
There are also CHARMM parameters that could be adapted:

(2) The reason I ask question (1) is that force field parameters generally
should obviate the need for distance restraints: Fe4S4 clusters are pretty
rigid objects, and don't move around much.

> I got to repeat every IAT parameters 4
> times (one per each cluster of the protein) and if I got to define every
> single bond of the Fe4-S4 cubane.

You would need a separate set of parameters for each of the four clusters.
Whether you need distance restraints for every bond is not clear: I've never
used such restraints myself.

...good luck...dac

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Received on Tue Jul 28 2015 - 18:00:02 PDT
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