Re: [AMBER] TIP3p lennard jones parameters

From: David A Case <david.case.rutgers.edu>
Date: Fri, 25 Aug 2017 16:17:08 -0400

On Fri, Aug 25, 2017, Lizelle Lubbe wrote:

> I noticed that the TIP3P parameters in this file do not correspond to
> the literature (radius 3.15061; well depth 0.6364)
> My values are 1.7683 and 0.1520 respectively.

Your "literature" values are sigma (in ) and epsilon (in kJ/mol). Amber
uses Rmin/2 (in ) and epsilon in kcal/mol. If you convert to what
Amber uses, you will find that they match.

>
> If not, how can I increase the verbosity in parmed.py to come to the
> bottom of this?

I agree that there are situations where it would be quite helpful if
parmed could print more information when it finds problems. Volunteers
are hereby solicited.

>
>
> source leaprc.ff14SB

General advice: upgrade to AmberTools17. Second, if you think that your
water model might be leading to off-diagonal LJ parms, do some exploring:
make a prmtop with just water (for example), and see what parmed says. Keep
adding in components one by one to see if you can isolate the problem.

...good luck....dac



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 25 2017 - 13:30:06 PDT
Custom Search