[AMBER] Help With tinker_to_amber

From: Angelo Rossi <angelo.raymond.rossi.gmail.com>
Date: Sat, 10 Mar 2018 13:49:03 -0500

Hello Everyone:

I am hoping that someone on the list can help me.

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 tried tinker-to-amber with a molecule using Amber frcfieldfile =

 found a-axis = 90.000000000000000
 num_xyz_atoms = 331
 numres = 40
 num_atoms = 331
 vdw: num_vdw_types = 6
 num_bonds = 324
 no success finding Urey-Bradley!
 num_tot_angles = 606
 num regular, trigonal angles = 606 0
 no success finding Out-of-Plane Bends
 numtor = 804
 num1,num_torsions = 702 774
 no success finding Stretch-Torsions
 no success finding Pi-Orbital Torsions
 no success finding Stretch-Bends!
 no success finding Torsion-Torsions
 num_molecules = 25
 no success finding Polarizable Multipoles!
 no success getting Dipole Polarizability Parameters
 forcefield for modified for Tinker and it works flawlessly producing Amber
prmtop and inpcrd files.

But, I would like tinker_to_amber to work with other Tinker forcefields, if
possible. I have a Tinker .xyz file, a Tinker .analout file, and a Tinker
modified amber99.prm file.

Here is the output for tinker_to_amber execution:

* frcfieldfile =
 found a-axis = 90.000000000000000 num_xyz_atoms =
331 numres = 40 num_atoms = 331 vdw: num_vdw_types
= 6 num_bonds = 324 no success finding
Urey-Bradley! num_tot_angles = 606 num regular, trigonal angles
= 606 0 no success finding Out-of-Plane Bends numtor
= 804 num1,num_torsions = 702 774 no success
finding Stretch-Torsions no success finding Pi-Orbital Torsions no success
finding Stretch-Bends! no success finding Torsion-Torsions num_molecules
= 25 no success finding Polarizable Multipoles! no success
getting Dipole Polarizability Parameters *
As you can see*, *it proceeds far along but wants more information about
other force field components.

Is there a way to modify the tinker_to_amber source code to allow for force
fields other than amoebapro13.prm to work?

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.

I would really appreciate your help and input so that I can go smoothly
from Tinker to Amber.

Thanks so much.

Kind regards,

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Received on Sat Mar 10 2018 - 11:00:02 PST
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