Re: [AMBER] A question about force-field parameters for organic compounds related to the purchase of AMBER-Certified EXXACT machine

From: Ross Walker <>
Date: Sun, 3 Jun 2018 13:02:23 -0400

Hi Jing,

I'll add to what Dave says in that if you can build a PSF file (Charmm style) then you could also convert that to a prmtop and inpcrd to run with AMBER using parmed that comes with AmberTools.

That said I 'think' OPLS3 is encrypted so you don't know what the underlying parameters are and thus it will only work in Desmond - I could be wrong though. On the other hand I'd be very wary of using a force field that you can't see the parameters for an so are unable to reproduce the results in other packages so you might be better with GAFF.

Either way as Dave says the process is highly automated and easy to use. You can either use GAFF plus an AMBER protein force field like FF14SB and/or a lipid force field like Lipid17 - or you can use a Charmm variant create a PSF file (either with Charmm or VMD for example) and then convert that to AMBER format input files with Parmed.

Good luck,

All the best

> On Jun 3, 2018, at 12:21, David A Case <> wrote:
> On Fri, Jun 01, 2018, Jing Wang wrote:
>> I am thinking to get the AMBER Certified Workstation currently put forth
>> by Exxact Corp, because the speed is very impressive to compare with
>> the Schrodinger Desmond that I am currently using. However, I remember
>> that in my old days the force-field parameters for small molecule
>> compounds needed to be developed each time to run AMBER or CHARMm. I
>> wonder what is the situation now. Can I get the program that generates
>> or help the user to generate these parameters? The situation with
>> Desmond/Schrodinger suite is that the GUI automatically generates or
>> assigns OPLS3 force-field to any compounds and at the user's choice, a
>> Force-Field Builder module can generate torsional angle profiles to new
>> chemotypes effortlessly. Can you tell me what is the situation for AMBER
>> and whether or not the whole process is available for an industrial
>> user?
>> I talked with Exxact Corp people and they said that I have to ask
>> you this question. They do not know if the code pre-installed on the
>> machines is good enough. I would greatly appreciate if you can answer my
>> question and help me make a decision.
> Amber has a very automated procedure, built on the generalized Amber
> force field (GAFF2) procedure. The basics are described in this
> tutorial:
> It is straightforward to script this procedure into a virtual screening
> (or other) workflow. Everything you need is available in AmberTools,
> and doesn't require any specialized hardware. (That is, you can check
> out how things work without needing anything more than a laptop
> computer.) We also have tools for optimizing individual torsion
> potentials (as opposed to taking the GAFF predictions), but these are
> less well automated.
> GAFF has been very widely used for more than a decade, so you can find
> lots of examples of its strengths and weaknesses; and of course, make
> your own tests. I am personally not "up" on comparisons between OPLS3
> and GAFF, but maybe others on the list can chime in.
> (If you have access to the OPLS3 parameterization, you could also
> consider converting those to Amber format.)
> ....dac
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Received on Sun Jun 03 2018 - 10:30:02 PDT
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