From: Brian Radak (brian.radak_at_gmail.com)
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 <hydrargyrumate_at_gmail.com>
wrote:
> 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
> LONE PAIR PARTICLE 24".
> 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 <brian.radak_at_gmail.com> 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 <hydrargyrumate_at_gmail.com>
>> 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 <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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