Dear list users, good night.
First of all, sorry for kind of "hijacking" this thread for a related topic.
But since we are talking about automatic parametrization, and given that AMBER's FFs philosophy makes the torsion parameters (original topic of the thread) highly correlated to both electrostatic (for which amber already provides both resp and pyresp) and van der Waals parameters, can I ask if someone has similar information on automated tools for (amber compatible) Lennard-Jones potentials parametrization?
Thanks lot in advance,
Jones
Em 17 de setembro de 2024 03:25:30 BRT, Nikolay Kuzmich via AMBER <amber.ambermd.org> escreveu:
>Dear David,
>
>thank you for your answer!
>
>Kind regards
>
>Nick
>
>________________________________
>From: David A Case <dacase1.gmail.com>
>Sent: Monday, September 16, 2024 5:54:02 AM
>To: Nikolay Kuzmich; AMBER Mailing List
>Subject: Re: [AMBER] Forcefield Builder analogs in Amber
>
>Caution: External Sender. Do not click on links or open attachments unless you recognize the sender.
>
>
>On Sun, Sep 15, 2024, Nikolay Kuzmich via AMBER wrote:
>
>>I wonder if there is something similar to Schrödinger's Forcefield Builder
>>in the Amber package for QM torsion parameters fitting. Is that paramfit
>>utility? Extensive comments are appreciated.
>
>I've not used the Schrodinger product you mention, but using QM to do a
>bespoke fitting for torsion parameters is a common task, and Amber users
>over the years have created a variety of tools for this.
>
>The paramfit utility is described in Chap 16 of the Amber 2024 Reference
>Manaul, and there is no point on expanding on that in an email.
>
>Chap 17 describes mdgx, which is a much more elaborate tool for force field
>development, with a larger associated learning curve. Look for the
>FitTorsion options in that Chapter if you are mainly interested in fitting
>torsions.
>
>Another recent tool, (which I have never used myself) is described here:
>
>https://chemrxiv.org/engage/chemrxiv/article-details/66df56e9cec5d6c1429f22e9
>
>Note that this package is not a part of Amber, and has its own software license
>agreement: be sure to see if that fits your needs.
>
>Others on the list may wish to chime in here: I know the folks that
>developed the packages listed above pretty well, but am far from an expert
>here.
>
>...hope this helps....dac
>
>
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Received on Tue Sep 17 2024 - 02:30:02 PDT
