Re: NAMD support for lone pairs

From: Tabitha Nobel (hydrargyrumate_at_gmail.com)
Date: Mon Mar 11 2019 - 18:10:43 CDT

My input PDB to parameterize with CHARMM did not include the lone pair. The
lone pair information was in the stream file, but I had to explicitly list
it in the input file for CHARMM. So I would have to renumber the resulting
PSF/PDB atoms. Do you know of a way I can do this automatically and not by
hand?

On Mon, Mar 11, 2019 at 2:39 PM Brian Radak <brian.radak_at_gmail.com> wrote:

> Ah, I think I see the problem now that I look at your PSF more closely,
>
> NAMD, I believe, requires lonepairs to be close to their parents (right
> after, unless there is also a Drude particle) in the PSF, or at least this
> is a convention of the CHARMM force fields. You similarly have all of your
> hydrogens at the end of the residue rather than near their associated heavy
> atoms.
>
> Was this molecule parameterized via CHARMM-GUI also? I've heard of
> ParamChem being sensitive to atom ordering and connectivity, so it might be
> worthwhile for you to reorganize the atoms in your input PDB. Without using
> mol2 format I don't know how you would get bonded information - maybe
> proximity in ordering is used heuristically in this case?
>
> On Mon, Mar 11, 2019 at 5:30 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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