From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Mar 08 2019 - 14:14:36 CST
This should be supported now for a valid PSF (did you try it and have it
The current lack of functionality is in the RTF parser inside psfgen, so
that you cannot yet build these PSFs. I would recommend CHARMM-GUI for that
purpose, although there are plans to support this in the future.
On Fri, Mar 8, 2019, 12:10 PM Tabitha Nobel <hydrargyrumate_at_gmail.com>
> 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,
> 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.
>> On Thu, Mar 7, 2019 at 9:27 PM Tabitha Nobel <hydrargyrumate_at_gmail.com>
>>> Dear NAMD developers,
>>> Are CGenFF lone pairs supported in NAMD version 2.13? This question is
>>> similar to the one asked here
>>> 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,
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