Re: [AMBER] Help With tinker_to_amber

From: David A Case <>
Date: Sat, 10 Mar 2018 15:57:07 -0500

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

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Received on Sat Mar 10 2018 - 13:00:01 PST
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