Thanks David for the prompt reply.
Since that cluster is a remote cluster so I am not sure whether I am
allowed to install any program there or not, but anyway I will inquire
about it.
I have already done the MD simulation of metal (monoatomic) ion bound
protein, employing non-polarizable force field and 12-6-4 ion parameter.
Now I want to compare it with polarizable MD simulation, since three
negatively charged amino acids are interacting with that metal ion.
Thanks
On Tue, Aug 8, 2017 at 1:19 PM, David A Case <dacase.chem.rutgers.edu>
wrote:
> 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
>
> --
>
> ====================================================================
> David A. Case | david.case.rutgers.edu
> Dept. of Chemistry & Chemical Biology |
> Rutgers University | office: +1-848-445-5885
> 174 Frelinghuysen Road, Rm. 208b | cell: +1-609-751-8668
> Piscataway, NJ 08854 USA | web: casegroup.rutgers.edu
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Received on Tue Aug 08 2017 - 06:00:03 PDT
