Re: NAMD support for lone pairs

From: Tabitha Nobel (hydrargyrumate_at_gmail.com)
Date: Tue Mar 12 2019 - 11:11:39 CDT

I'm not sure if the error is with CGenFF or rather with how the PSF file is
generated. When updating VMD's psfgen to support lone pairs, it should just
be a matter of ensuring that there is an explicit bond present in the PSF.
Thanks a lot Brian for your help!

Also replying to JC's comment, it would be worth following up with the
others. While CHARMM didn't crash with the PSF without the explicit lone
pair bond, the lone pair didn't stay colinear with its parent chlorine
atom.

On Tue, Mar 12, 2019 at 6:35 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> Are you sure that it’s not an error in CGenFF or some other oversight? I
> have trouble imagining them putting a free lone pair in there. That CHARMM
> doesn’t crash probably just means no one thought to check it. I would
> follow up with Alex et al. before writing a lot of code to support it.
>
> Best,
> JC
>
> On Mar 12, 2019, at 8:50 AM, Brian Radak <brian.radak_at_gmail.com> wrote:
>
> Tabitha,
>
> Thanks for updating us with the results
> of those tests! Apparently my previous guess regarding atom order was
> incorrect (though I will still contend this is a good idea and best
> practice).
>
> To summarize - NAMD does not appear to like PSFs that do not contain an
> explicit bond to lonepairs, but CHARMM accepts them just fine. The
> canonical force fields appear to always include those bonds, but CGenFF may
> not when adding a lonepairs on chlorine (any halogen?). The developers will
> have to discuss how best to address this odd edge case.
>
> Thanks for working through this with us,
>
> Brian
>
> On Mon, Mar 11, 2019, 9:01 PM Tabitha Nobel <hydrargyrumate_at_gmail.com>
> wrote:
>
>> Adding the bond indices and incrementing the NBOND count by one worked! I
>> tried it also on the PSF/PDB pair that did not have the lone pair close to
>> its parent, and that worked as well. The results of the minimization look
>> reasonable.
>>
>> On Mon, Mar 11, 2019 at 5:27 PM Brian Radak <brian.radak_at_gmail.com>
>> wrote:
>>
>>> That's odd. The BOND command in the Residue definition should cause the
>>> PSF to have a bond entry - regardless the ordering.
>>>
>>> You can try adding a manual bond by incrementing the ! NBOND count by
>>> one and adding two extra bond indices to the list (note that the PSF
>>> indices start at one). This is not an ideal solution, but hopefully it will
>>> work.
>>>
>>> Can you send me your initial pdb offline so that I can play with this?
>>> We are looking to support this kind of construction in psfgen and this kind
>>> of lonepair support might be one of the first things we can get going.
>>>
>>>
>>> On Mon, Mar 11, 2019, 7:51 PM Tabitha Nobel <hydrargyrumate_at_gmail.com>
>>> wrote:
>>>
>>>> Hi Brian,
>>>>
>>>> I tried renumbering the atoms in my PSF and PDB file as you suggested.
>>>> I also added the BOND statement in my stream file.
>>>> However, NAMD is complaining that the lone pair is an isolated
>>>> particle. My edited files are attached in this email.
>>>> Do you other ideas as to what might be the problem?
>>>>
>>>> Best,
>>>> Tabitha
>>>>
>>>> On Mon, Mar 11, 2019 at 4:10 PM Tabitha Nobel <hydrargyrumate_at_gmail.com>
>>>> wrote:
>>>>
>>>>> 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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