Re: [AMBER] force-filed parametrization for dichloromethane

From: David A Case <>
Date: Fri, 23 Mar 2018 07:43:27 -0400

On Wed, Mar 21, 2018, daniele selli wrote:
> I am pretty new to the AMBER code, but I am trying to derive new parameters
> for dichloromethane (DCM), which I would like to use as a solvent for my
> systems.
> Following the AMBER Advanced tutorial 27 for the PET polymer,
> I was able to generate *.prepi parameters for DCM. I used Gaussian to
> perform an ESP analysis and then a RESP fit with antechamber.
> However, to test them I have generated a DCM box and performed NPT
> molecular dynamics to be sure to have the proper density. My box shrink of
> a
> 7%, meaning that my parameters give me a too dense DCM.
> Do any of you know what I am doing wrong? It is something regarding
> van der Waals interactions I am neglecting?

You might try using gaff2, which generally has better optimized
Lennard-Jones radii (and hence better liquid densities) than the
original gaff.

Add the "-at gaff2" flag to antechamber, the "-s 2" flag to parmchk2 (if
you use that), and change the file to "source leaprc.gaff2".

This may or may not solve your problem: force fields generated by
antechamber should be considered as trials, and sometimes need hand
modification. I'm guessing you might need to adjust the LJ radius for
chlornine. But try gaff2 first.

...good luck....dac

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Received on Fri Mar 23 2018 - 05:00:03 PDT
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