Re: [AMBER-Developers] Discussion towards removing tip3p parameters from protein, RNA & DNA ff

From: David A Case <>
Date: Tue, 9 Mar 2021 12:06:25 -0500

On Tue, Mar 09, 2021, Kellon Belfon wrote:
>Therefore I started my test by removing all mentions of HW and OW
>parameters from these parmxx.dat files. By doing this approach users will
>have to explicitly source the tip3p leaprc (leaprc.water.tip3p) in order to
>get the HW and OW parameters for tip3p.

Kellon: this is great!

> - If anyone else does not object (big possibility I am missing some
> knowledge on how things were done in amber in the past) then I propose to
> regenerate the topology and leap log files for the test failures with
> NTYPES and NPHB differences.
> - I also proposed to change the for the tests that fail to
> source leaprc.water.tip3p.

I'm in favor of both of these, but might also be missing something...

>One of the test case $AMBERHOME/AmberTools/test/leap/Run.cmds tend to give
>different water coordinates and number of water molecules when source
>leaprc.water.tip3p vs keeping the tip3p parameters in the parm10.dat file

This one might be worth tracking down: looks like "solvateBox" is somehow
changing its behavior(?) I could see that being a problem if people were
trying to reproduce old workflows. How big is the difference in numbers of


AMBER-Developers mailing list
Received on Tue Mar 09 2021 - 09:30:01 PST
Custom Search