On Tue, Aug 08, 2017, sangita kachhap wrote:
> I want to do MD simulation of metal ion bound protein using polarizable
> force field. TINKER is not available in the cluster, thus, I can not use
> AMOBEA. Is there another polarizable force field available in AMBER16?
Tinker is easy to install via github, and doesn't require any special
permissions. OpenMM also supports the AMOEBA force field, and CHARMM has
an up-to-date polarizable force field as well.
[All of the above, however, have significant learning curves. Depending
on what metal ion you are considering, and how it is bound to the protein,
you might wish to consider the 12-6-4 ion parameters in Amber. These are,
however, only available for some monatomic ions.]
...good luck....dac
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Received on Tue Aug 08 2017 - 04:30:02 PDT
