- Posts: 2
Backmapping of ERG - problems with cis/trans and chirality
- F.Keller
-
Topic Author
- Offline
- Fresh Boarder
Less
More
3 years 5 months ago #8752
by F.Keller
Backmapping of ERG - problems with cis/trans and chirality was created by F.Keller
Dear Martini users,
I am trying to backmap a lipid bilayer containing ergosterol. As far as I know, there is no mapping file for ERG created yet, am I correct? So I tried to create it myself using cholesterol mapping as a basis.
Unfortunately, this task appears not to be that straightforward:
I tried to simply set all the rules according to the target ergosterol configuration. As this didn't work, I tried using the more implicit approach and allow for a correct environment just like it is done in the mapping file for PL cis double bonds and unfortunately, this didn't work either. I appreciate any help, comments or doubts! :-) Maybe you have a hint on how to proceed, or maybe these problems are just the reason why there is no mapping file for ERG yet.
For the backmapping I used the latest script from github.com/Tsjerk/Backward
All the files I used, along with a script to reproduce the backmapping, you can find following uni-muenster.sciebo.de/s/HKUjw3QRnQGZJZw
My approach for the ergosterol mapping file resides in Mapping/ERGO.charmm36.map
Best,
Fabian
I am trying to backmap a lipid bilayer containing ergosterol. As far as I know, there is no mapping file for ERG created yet, am I correct? So I tried to create it myself using cholesterol mapping as a basis.
Unfortunately, this task appears not to be that straightforward:
- The double bond in the short chain flips to cis for some molecules
- Some chiral centers are not always maintained correctly, namely C20 and C24, and (seldomly) even C3. (names from common/charmm cholesterol naming convention)
I tried to simply set all the rules according to the target ergosterol configuration. As this didn't work, I tried using the more implicit approach and allow for a correct environment just like it is done in the mapping file for PL cis double bonds and unfortunately, this didn't work either. I appreciate any help, comments or doubts! :-) Maybe you have a hint on how to proceed, or maybe these problems are just the reason why there is no mapping file for ERG yet.
For the backmapping I used the latest script from github.com/Tsjerk/Backward
All the files I used, along with a script to reproduce the backmapping, you can find following uni-muenster.sciebo.de/s/HKUjw3QRnQGZJZw
My approach for the ergosterol mapping file resides in Mapping/ERGO.charmm36.map
Best,
Fabian
Please Log in or Create an account to join the conversation.
Time to create page: 0.097 seconds