From owner-chemistry@ccl.net Fri Jul 28 09:25:00 2017
From: "Ramon Crehuet ramon.crehuet[#]iqac.csic.es" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: Run a molecular dynamics with Tinker in explicit water
Message-Id: <-52912-170728091418-31895-a9pyWF3v1DMhUz2smVLxUg{}server.ccl.net>
X-Original-From: "Ramon  Crehuet" <ramon.crehuet~~iqac.csic.es>
Date: Fri, 28 Jul 2017 09:14:16 -0400


Sent to CCL by: "Ramon  Crehuet" [ramon.crehuet_+_iqac.csic.es]
Dear CCLers,
I would like to run a simulation of a peptide in a water box using the AMOEBA 
polarizable force field with Tinker.
I have followed these steps:
1) Create the xyz file for the protein with protein and minimize it. Works. I 
used the amoebapro13 force field for proteins.
2) Create a box of water molecules from the water.xyz and water.key with xyzedit 
example file. It works, but this uses the water14 force field.
3) introduce the peptide in the water box with xyzedit. This generates an xyz, 
but when I try to minimize it, it complains that there many missing parameters. 
Curiously, despite I define the force field to be amoebapro13, the missing 
parameters correspond to peptide atoms, not the water atoms.

We also tried to create the water box with the amoebapro13 force field, but then 
it also complains that there are missing parameters.

Could somebody tell me the correct steps to run this MD?
Thanks in advance,
Ramon