[AMBER] restraint simulation

From: <abhay.strubi.ox.ac.uk>
Date: Wed, 15 Jun 2011 11:51:29 +0100 (BST)

Dear AmberUsers,

We are interested in binding energy calculations of two very large proteins. We know that only the residues that are around 15A from the inter-protomeric interface are involved in interactions (keeping two proteins together).

Is it possible to run the simulation with restraints on everything above 15A radius of the interface and calculate the binding energy? Also I was confused with NPT and NVT ensembles, as we want to use restraints in simulation is it fine to us NVT ensemble?

Any replies will be very helpful.


Abhay Kotecha
DPhil Student
Division of Structural Biology
Henry Wellcome Building for Genomic Medicine,
Oxford, OX3 7BN, UK
Ph: +44 (0)1865 287541
Mobile: +44 (0)7702794123

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Received on Wed Jun 15 2011 - 04:00:11 PDT
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