Re: NAMD support for lone pairs

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Mar 11 2019 - 16:30:56 CDT

I would probably not recommend trying to manually alter a PSF (though it is
possible).

I'm just confused by this behavior from CHARMM-GUI. It would be nice to
know if their output can be run with CHARMM natively, which could indicate
an overly strict response from NAMD (and maybe require a change).

On Mon, Mar 11, 2019 at 5:02 PM Tabitha Nobel <hydrargyrumate_at_gmail.com>
wrote:

> Hi Brian,
>
> Would the parent be defined in the bonds section of the PSF? Is this
> something I can manually add?
>
> I haven't run it in CHARMM, no, but if you think it's helpful I can try to
> get that going. Ultimately I would want to be using NAMD though.
>
> -Tabitha
>
> On Mon, Mar 11, 2019 at 11:41 AM Brian Radak <brian.radak_at_gmail.com>
> wrote:
>
>> 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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