Re: NAMD support for lone pairs

From: Brian Radak (
Date: Mon Mar 11 2019 - 19:27:48 CDT

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 <>

> 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 <>
> 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 <>
>> 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 <>
>>> 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 <>
>>>> 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 <>
>>>>> 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 <
>>>>>>> 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
>>>>>>> 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 <>
>>>>>>> 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 <
>>>>>>>>> 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 <>
>>>>>>>>> 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 <
>>>>>>>>>>> wrote:
>>>>>>>>>>> Dear NAMD developers,
>>>>>>>>>>> Are CGenFF lone pairs supported in NAMD version 2.13? This
>>>>>>>>>>> question is similar to the one asked here
>>>>>>>>>>> <>,
>>>>>>>>>>> but I saw in the release notes
>>>>>>>>>>> <> 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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