Re: [AMBER] Help With tinker_to_amber

From: Angelo Rossi <>
Date: Sun, 11 Mar 2018 17:48:15 -0400

> Date: Sat, 10 Mar 2018 15:57:07 -0500
> From: David A Case <>
> Subject: Re: [AMBER] Help With tinker_to_amber
> To: AMBER Mailing List <>
> Message-ID:
> <20180310205707.7byonf5ngty3ovmz.vpn-client-
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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,

AMBER mailing list
Received on Sun Mar 11 2018 - 15:00:03 PDT
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