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 Å) and epsilon (in kJ/mol). Amber
uses Rmin/2 (in Å) 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
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Received on Fri Aug 25 2017 - 13:30:06 PDT
