Re: [AMBER] What forcefield does the DHFR JAC benchmark system use?

From: David Cerutti <>
Date: Sat, 25 Nov 2017 15:44:19 -0500

That's an interesting question. I am looking through the assembled prmtop
(which unfortunately I can't pick apart with my tools because it is in the
old format, with no cards preceding each section).

It uses TIP3P water.
It uses atomic charges consistent with one of the Cornell force fields.
It uses atom types that are found in the Cornell line of force fields,
prior to the introduction of new C-beta types in ff10 and ff14SB.

I'm trying to go through the torsion amplitudes and cross-reference them
with values found in each parm??.dat file or associated frcmods--it's tough
going, and none of the files are matching some of the amplitudes--tleap may
have done something that combines things or evaluates combinations of
parameters that I am unaware of.

My best guess is that it is something pre-Cornell, from before parm94.dat
as not even that file holds all of the parameters that this thing seems to


On Sat, Nov 25, 2017 at 2:12 PM, John Chodera <> wrote:

> Hi all,
> We were curious if anyone knew which AMBER forcefield was used in the DHFR
> JAC benchmark system from the Amber14 benchmark suite
> (Amber14_Benchmark_Suite/PME/JAC_production_NPT).
> We've looked for details but have been unable to find them.
> Thanks!
> John
> P.S. Apologies if this was mistakenly sent twice! I've been having trouble
> with my email recently.
> --
> John D. Chodera
> Assistant Faculty Member, Computational Biology
> Memorial Sloan-Kettering Cancer Center
> email: j <>
> office: 646.888.3400
> fax: 510.280.3760
> mobile: 415.867.7384
> url:
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Received on Sat Nov 25 2017 - 13:00:03 PST
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