Re: NAMD support for lone pairs

From: Tabitha Nobel (hydrargyrumate_at_gmail.com)
Date: Mon Mar 11 2019 - 17:15:45 CDT

Just confirmed that CHARMM does successfully minimize the given PSF and
coordinates.
Also to clarify, the PSF was generated using CHARMM and not CHARMM-GUI.

On Mon, Mar 11, 2019 at 2:30 PM Brian Radak <brian.radak_at_gmail.com> wrote:

> 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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