> Date: Sat, 10 Mar 2018 15:57:07 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Help With tinker_to_amber
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20180310205707.7byonf5ngty3ovmz.vpn-client-
> 172-16-8-64.rutgers.edu>
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>
> On Sat, Mar 10, 2018, Angelo Rossi wrote:
> >
> > I would very much like to create amber prmtop and inpcrd files for input.
> > I have a tinker parameter file based on amber99.prm, but modified to
> > include parameters for a metal cluster with attached ligands.
>
> > I have a Tinker .xyz file, a Tinker .analout file, and a Tinker
> > modified amber99.prm file.
>
> It's not clear to me what you are trying to do here: is you target force
> field one with Amoeba-like terms, or is it a standard (fixed charge,
> atom-based monopoles) force field like amber99.prm itself?
>
> The tinker_to_amber program is solely devoted to converting Amoeba force
> field descriptions into an Amber-compatible format. In spite of its
> name, it is not a general-purpose way to convert tinker files to Amber.
>
> > Is there a way to modify the tinker_to_amber source code to allow for
> force
> > fields other than amoebapro13.prm to work?
>
> It might be doable, but I wonder if it is not better to consider
> creating mol2 and frcmod files by hand for your metal cluster and
> ligands. One advantage would be to advance beyond Amber's f99
> forcefield, which is really quite poor by modern standards.
>
> If you do have polarizabilities and multipoles, you might also consider
> using tinker itself or openMM for the simulation: neither of these
> options requires a conversion to Amber formats.
>
> >
> > Right now, I have the binary version of AmberTools. When I had the
> source
> > version of AmberTools (which I deleted because of python conflicts), I
> > could not find the source for tinker_to_amber.
>
> Look in $AMBERHOME/AmberTools/etc.
>
> ...good luck....dac
>
>
>
> Dear David Case:
Thanks so much for your reply. Yes, I was actually trying to take a
shortcut to obtain prmtop and inpcrd files by using the tinker_to_amber
utility. It has a more specific use than I considered.
And I will do as you say by creating mol2 and frcmod files by hand.
Thanks so much for your help in this.
Kind regards,
Angelo
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Received on Sun Mar 11 2018 - 15:00:03 PDT
