Previous Thread
Next Thread
Print Thread
#38307 07/23/21 05:08 PM
Joined: Jul 2021
Posts: 2
A
an_a Offline OP
Forum Member
OP Offline
Forum Member
A
Joined: Jul 2021
Posts: 2
I am working with a small molecule ligand that contains selenium. I am having trouble parameterizing it using CGenFF/ParamChem. I can't get it to successfully run through any of the parameterization options in CHARMM-GUI either. Does anyone have *any* experience with/advice regarding parameterizing and running MD of selenium containing small molecules? Any hints/suggestions would be very much appreciated!

ana

Joined: Sep 2003
Posts: 8,597
Likes: 12
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,597
Likes: 12
With a quick web search I found

Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS.
Jennifer Loschwitz, Anna Jäckering, Monika Keutmann, Maryam Olagunju, Olujide O.Olubiyi, Birgit Strodel
Data in Brief,Volume 35, April 2021, 106948

They used GAFF to derive models using S instead of Se, defined some modified Se parameters, and changed S to Se after all the model building, which may be an approach to use with CGenFF and CHARMM-GUI. The Se parameters in that paper may or may not be transferrable, and should be validated before use with CHARMM force fields.


Rick Venable
computational chemist

Joined: Jul 2021
Posts: 2
A
an_a Offline OP
Forum Member
OP Offline
Forum Member
A
Joined: Jul 2021
Posts: 2
rmv,

Thank you very much for sharing this nice idea from the paper. This is perhaps what I will do as well. Seems like Se parameters are not available in many of the popular forcefields.

ana


Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.011s Queries: 20 (0.008s) Memory: 0.7368 MB (Peak: 0.7809 MB) Data Comp: Off Server Time: 2022-07-03 11:41:52 UTC
Valid HTML 5 and Valid CSS