[AMBER] Using multiple distance restraints or creating exclusion sphere

From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
Date: Mon, 13 Jul 2020 01:20:16 +0000

Hi everyone,

I'm hoping you could help me with something. I am running a membrane channel simulation, and I would like to make sure that ions (Na+, specifically) doesn't get into the selectivity filter of this channel, so I can see what happens when an ion is not present. I have done distance restraints before with one molecule, but I would like to exclude ALL Na+ ions from a particular area. Is there a way to do that in Amber? Would it be with adding multiple distance restraints? If so, how do I do multiple distance restraints?

Best wishes


Dr. Amanda Buyan

Postdoctoral Fellow, Corry Lab

Research School of Biology

134 Linnaeus Way

Canberra, ACT 2601

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Received on Sun Jul 12 2020 - 18:30:04 PDT
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