Re: NAMD support for lone pairs

From: Tabitha Nobel (hydrargyrumate_at_gmail.com)
Date: Mon Mar 11 2019 - 16:02:11 CDT

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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