From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Mon Feb 22 2021 - 20:12:06 CST
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<mailto: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<mailto:gumbart_at_physics.gatech.edu>> wrote:
It’s distributed with more recent VMD builds.
Best,
On Feb 22, 2021, at 8:25 PM, Gumbart, JC <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>> wrote:
paramchem can do it: https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!qWw5n-IteGWCR0SyAlDUHjOReMvsCCfH_Ra08P9O6Ya_gkINhwBlC314sHU9k9qPjQ$ <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*7Cb5c4e4a2efef424e48ab08d8d79fd190*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637496429150360600*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=VzdcH3xhsU81YGvwMY9wPQibDsoGV*2FJ1hJQf4m1*2BcBw*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!qWw5n-IteGWCR0SyAlDUHjOReMvsCCfH_Ra08P9O6Ya_gkINhwBlC314sHU9MuTPDg$ >
Best,
On Feb 22, 2021, at 7:49 PM, David Hardy <dhardy_at_ks.uiuc.edu<mailto: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,
On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <ccs0019_at_mix.wvu.edu<mailto:ccs0019_at_mix.wvu.edu>> wrote:
Hi David,
Thanks again for helping me
Chathuranga
Chathuranga Siriwardhana
On Mon, Feb 22, 2021 at 7:26 PM David Hardy <dhardy_at_ks.uiuc.edu<mailto:dhardy_at_ks.uiuc.edu>> wrote:
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,
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: Fri Dec 31 2021 - 23:17:10 CST
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
JC
JC
Dave
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.
Justin Legleiter Laboratory
West Virginia University
Department of chemistry
Clark Hall, Room 561
Morgantown, WV 26505
Hi Chathuranga,
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<mailto:dhardy_at_ks.uiuc.edu>, http://www.ks.uiuc.edu/~dhardy/