Re: NAMD support for lone pairs

From: Tabitha Nobel (hydrargyrumate_at_gmail.com)
Date: Fri Mar 08 2019 - 11:10:13 CST

Hi Brian,

Thank you very much for your response. This might be a naive question, but
if I have a chloro group with a lone pair generated from CGenFF, is there a
way I can convert that to a currently supported format from NAMD?

Thank you,
Tabitha

On Fri, Mar 8, 2019 at 7:45 AM Brian Radak <brian.radak_at_gmail.com> wrote:

> Hi Tabitha,
>
> As of 2.13 there should be full support for all lonepair types* that
> exist in currently published/released* *CHARMM force fields*, both fixed
> charge and Drude. This includes the "bisector" lonepairs on water and
> carbonyls as well as the "collinear" lonepairs most associated with
> halogens (e.g. chlorobenzene). Furthermore, the old "lonepair on" keyword
> should be essentially deprecated and instead auto-detected based on the PSF
> contents (it should be very obvious if this does not work). However, NAMD
> does not yet support all CHARMM compatible lonepairs because they are not
> defined in the PSF standard.
>
> Cheers,
> BKR
>
> On Thu, Mar 7, 2019 at 9:27 PM Tabitha Nobel <hydrargyrumate_at_gmail.com>
> wrote:
>
>> Dear NAMD developers,
>>
>> Are CGenFF lone pairs supported in NAMD version 2.13? This question is
>> similar to the one asked here
>> <https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2018-2019/0992.html>,
>> but I saw in the release notes
>> <https://www.ks.uiuc.edu/Research/namd/2.13/features.html> that there
>> was improved lone pair support, and it wasn't clear to me whether that was
>> only for the Drude force field.
>>
>> Thank you,
>> Tabitha
>>
>

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