From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Feb 23 2021 - 06:35:32 CST
Somewhere in NAMD 2.13 development we dropped the use of dummy bonds to
lonepairs and exclusively took that information from the PSF lonepair host
section (NUMLPH). These sections were otherwise redundant at best or
contradictory at worst.
One thing that might still get goofed up is the "lonepairs on" command,
which should be auto toggled based on the PSF header. I'm pretty sure it
would be safe to add this to you config file.
HTH,
Brian
On Mon, Feb 22, 2021, 9:42 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:
> Please reply-all to keep the mailing list in your replies.
>
> As I recall, there shouldn’t be a bond parameter for it because it’s
> fixed. Something is likely still wrong with your PSF. You need to build
> it using PSFGen 2.0. It should be correct if you see a !NUMLP section, as
> Dave pointed out.
>
> Best,
> JC
>
> On Feb 22, 2021, at 9:30 PM, Chathuranga Siriwardhana <ccs0019_at_mix.wvu.edu>
> wrote:
>
> I have included the force field files from the C36 July release.
> Apparently it did not have the parameters for the CL LPH bond.
>
>
> *Chathuranga Siriwardhana*
> Justin Legleiter Laboratory
> West Virginia University
> Department of chemistry
> Clark Hall, Room 561
> Morgantown, WV 26505
>
>
> On Mon, Feb 22, 2021 at 9:12 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
> wrote:
>
>> You have to include the appropriate CGenFF force-field file as well.
>>
>> Best,
>> JC
>>
>> On Feb 22, 2021, at 9:07 PM, Chathuranga Siriwardhana <
>> ccs0019_at_mix.wvu.edu> wrote:
>>
>> Hi JC,
>> Thank you for the reply. I parameterized the molecule from the same
>> online GUI you mentioned above.
>> However my stream file created through the cgenff does not have bond
>> parameters for CL and LPH. Do you know how to fix it
>>
>> *FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 38 21)*
>>
>> Thanks again for your help
>> Chaturanga
>>
>> *Chathuranga Siriwardhana*
>> Justin Legleiter Laboratory
>> West Virginia University
>> Department of chemistry
>> Clark Hall, Room 561
>> Morgantown, WV 26505
>>
>>
>> On Mon, Feb 22, 2021 at 8:28 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
>> wrote:
>>
>>> Oops, I replied too fast. I was thinking of the parameters, not the
>>> PSF. The latest version of PSFGen ( >= 2.0) can handle it:
>>> https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf
>>> <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.ks.uiuc.edu*2FResearch*2Fvmd*2Fplugins*2Fpsfgen*2Fug.pdf&data=04*7C01*7Cgumbart*40physics.gatech.edu*7Cfe51710bd10a44c26fd308d8d7a30c5a*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637496442580473514*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=DRWnW0cldbGebK8FJkIo4FaDwsFrsUT8ZYHdm3*2B0wHY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!sAWNRPxKQeQ9Vr-YodvN7evq8h0Y95YmFj3JSN3sLcYx_RjtDj5D8PVUgq8LJUAPxQ$>
>>>
>>> It’s distributed with more recent VMD builds.
>>>
>>> Best,
>>> JC
>>>
>>> On Feb 22, 2021, at 8:25 PM, Gumbart, JC <gumbart_at_physics.gatech.edu>
>>> wrote:
>>>
>>> paramchem can do it: https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!ryfnj3SD9J_vYHxJ8jln6BETJxv5lhVo6xyEQ84t3JSilUe5ZhC5IVe6tHV8h3ajSA$
>>> <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fcgenff.umaryland.edu*2F&data=04*7C01*7Cgumbart*40physics.gatech.edu*7Cfe51710bd10a44c26fd308d8d7a30c5a*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637496442580483502*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=VrNoWA0XyAMhrolGxx5Kia6A7*2FUy5kn6*2F4Te48HS5wo*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!sAWNRPxKQeQ9Vr-YodvN7evq8h0Y95YmFj3JSN3sLcYx_RjtDj5D8PVUgq-mVEyMkg$>
>>>
>>> Best,
>>> JC
>>>
>>> On Feb 22, 2021, at 7:49 PM, David Hardy <dhardy_at_ks.uiuc.edu> wrote:
>>>
>>> Hi Chathuranga,
>>>
>>> No worries. I am replying back to the list because I don’t know the
>>> answer to your question.
>>>
>>> Can anyone on list recommend how to correctly create a PSF with lone
>>> pairs?
>>>
>>> Thanks,
>>> Dave
>>>
>>> On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <
>>> ccs0019_at_mix.wvu.edu> wrote:
>>>
>>> Hi David,
>>> Thank you so much for helping me with my issue. And I am really sorry
>>> that I replied to the wrong email. I subscribed to the mailing list today
>>> and I got confused with how it works :(
>>> Would you mind recommending a method to create the psf with lone pairs.
>>> I used VMD psfgen.
>>>
>>> Thanks again for helping me
>>>
>>> Chathuranga
>>>
>>>
>>>
>>>
>>>
>>>
>>> *Chathuranga Siriwardhana*
>>> Justin Legleiter Laboratory
>>> West Virginia University
>>> Department of chemistry
>>> Clark Hall, Room 561
>>> Morgantown, WV 26505
>>>
>>>
>>> On Mon, Feb 22, 2021 at 7:26 PM David Hardy <dhardy_at_ks.uiuc.edu> wrote:
>>>
>>>> Hi Chathuranga,
>>>>
>>>> It looks to me like NAMD is not treating your atom 37 as a lone pair.
>>>> The forces on lone pairs are distributed to their support atoms and then
>>>> set to zero, so I would expect lone pairs to have zero velocity (but I’m
>>>> having trouble finding that in the code).
>>>>
>>>> If you would post the top of your log file showing the configuration of
>>>> your system before simulation begins, we could see whether or not your
>>>> simulation has any lone pairs enabled.
>>>>
>>>> Thanks,
>>>> Dave
>>>>
>>>> --
>>>> David J. Hardy, Ph.D.
>>>> Beckman Institute
>>>> University of Illinois at Urbana-Champaign
>>>> 405 N. Mathews Ave., Urbana, IL 61801
>>>> dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
>>>> <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=http:*2F*2Fwww.ks.uiuc.edu*2F*dhardy*2F&data=04*7C01*7Cgumbart*40physics.gatech.edu*7Cfe51710bd10a44c26fd308d8d7a30c5a*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637496442580493508*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=WZyhQkW*2FbvF1Nhz10DzKhc6UOGNjUfkY9vIix8*2BzgaA*3D&reserved=0__;JSUlfiUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!sAWNRPxKQeQ9Vr-YodvN7evq8h0Y95YmFj3JSN3sLcYx_RjtDj5D8PVUgq9zUeGFkQ$>
>>>>
>>>> On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <
>>>> ccs0019_at_mix.wvu.edu> wrote:
>>>>
>>>> Thanks Jeff,
>>>> I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated
>>>> Thanks
>>>>
>>>>
>>>>
>>>> *Chathuranga Siriwardhana*
>>>> Justin Legleiter Laboratory
>>>> West Virginia University
>>>> Department of chemistry
>>>> Clark Hall, Room 561
>>>> Morgantown, WV 26505
>>>>
>>>>
>>>> On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer <jeffcomer_at_gmail.com> wrote:
>>>>
>>>>> What version of NAMD are you using? Versions earlier than NAMD 2.14
>>>>> don’t support halogen lonepairs.
>>>>>
>>>>> Jeff
>>>>>
>>>>>
>>>>> On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana <
>>>>> ccs0019_at_mix.wvu.edu> wrote:
>>>>>
>>>>>> Hi NAMD users,
>>>>>> I'm trying to see the interaction of a small molecule with a protein
>>>>>> in NAMD. As the simulation starts the following error appears;
>>>>>>
>>>>>> ERROR: Margin is too small for 1 atoms during timestep 1004.
>>>>>> ERROR: Incorrect nonbonded forces and energies may be calculated!
>>>>>> ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000,
>>>>>> atom 310 of 311 on patch 0 pe 1)
>>>>>> ERROR: Atoms moving too fast; simulation has become unstable (1 atoms
>>>>>> on patch 0 pe 1).
>>>>>> FATAL ERROR: Exiting prematurely; see error messages above.
>>>>>>
>>>>>> Atom 37 is a lone pair on Chlorine in the small molecule. Any help is
>>>>>> really appreciated.
>>>>>>
>>>>>> Thanks
>>>>>> Chathuranga
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> *Chathuranga Siriwardhana*
>>>>>> Justin Legleiter Laboratory
>>>>>> West Virginia University
>>>>>> Department of chemistry
>>>>>> Clark Hall, Room 561
>>>>>> Morgantown, WV 26505
>>>>>>
>>>>> --
>>>>>
>>>>> –––––––––––––––––––––––––––––––––––———————
>>>>> Jeffrey Comer, PhD
>>>>> Associate Professor
>>>>> Department of Anatomy and Physiology
>>>>> Kansas State University
>>>>> Office: P-213 Mosier Hall
>>>>> Phone: 785-532-6311
>>>>> Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!ryfnj3SD9J_vYHxJ8jln6BETJxv5lhVo6xyEQ84t3JSilUe5ZhC5IVe6tHXCV2PIFQ$
>>>>> <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2F*2Fjeffcomer.us__*3B!!DZ3fjg!oy19tN7QUSKcotZH8b_xfG1SoCSjFRxtAfeYKD73jGbd_OG5PSXl7j1cR8LcY4lt7w*24&data=04*7C01*7Cgumbart*40physics.gatech.edu*7Cfe51710bd10a44c26fd308d8d7a30c5a*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637496442580493508*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=8Wgcl5OLNqa3BNMvhyyjscHaBvrZrUtZ*2BT*2BNwBLeSA4*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!sAWNRPxKQeQ9Vr-YodvN7evq8h0Y95YmFj3JSN3sLcYx_RjtDj5D8PVUgq9UCcTuaQ$>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>
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