Re: NAMD support for lone pairs

From: Brian Radak (
Date: Mon Mar 11 2019 - 13:41:20 CDT

Hi Tabitha,

NAMD seems to interpret unbonded lonepairs as an error - there needs to be
one (and only one) entry in the PSF indicating the parent for that lonepair
(not just in the NUMLP block). I don't know if CHARMM includes this by
default or not.

I assume your PSF runs just fine in CHARMM?

On Fri, Mar 8, 2019 at 6:46 PM Tabitha Nobel <>

> Yes, I actually used CHARMM to build the PSF. When I tried the resulting
> files in a NAMD minimization, I got the error "FATAL ERROR: FOUND ISOLATED
> Do I need to specify anything in the configuration file about the lone
> pair? You mentioned the "lonepair on" keyword is deprecated, and I didn't
> see mention of anything else in the current user guide.
> I attached my stream file from CGenFF, the PSF/PDB files generated from
> CHARMM, and my NAMD input and output files.
> Is there other information I can provide that would shed more light on
> this problem?
> Thank you!
> On Fri, Mar 8, 2019 at 12:14 PM Brian Radak <> wrote:
>> This should be supported now for a valid PSF (did you try it and have it
>> not work?).
>> 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 <>
>> wrote:
>>> 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 <>
>>> 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 <>
>>>> wrote:
>>>>> 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
>>>>> <> 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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