normal Mapping DPC with backward.py

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
6 years 1 month ago #7544 by almeida
Mapping DPC with backward.py was created by almeida
Hi all,
I am doing some simulations of a membrane protein in detergent dodecylhosphatidylcholine (DPC). First, I was looking for a CG model of DPC but I couldn't find any, so I used insane.py to generate a CG model for DPC. For this I modified the script as following in the Phospholipids definition section:

## NEW - Dodecylhosphatidylcholine (DPC) detergent corresponding to atomistic C12:0 tail
"DPC": (moltype, " - - - NC3 - PO4 - C1A C2A C3A - - - - - - - - - - "),

(It's this correct?)

With the generated .gro file I builded the protein/micelle system with Packmol. I used the .itp file for DPC for the simulations. The production runs worked very well. Now, I want to map the protein/micelle system back to atomistic resolution (gromos), but backward.py script doesn't map DPC. Could you help me in this task? I though to modify the map file of DLPC, leaving the C12:0 chain and removing the glycerol and the second alkyl chain.

Thanks a lot in advance.

Best wishes

Yasser

Please Log in or Create an account to join the conversation.

More
6 years 1 month ago - 6 years 1 month ago #7545 by riccardo
Replied by riccardo on topic Mapping DPC with backward.py
I do not know lipids that much to be able to tell you whether what you suggest at the end of the post is correct. Looking at several examples of mapping files available in the Martini lipidome should help you understand that, though. You should then be able to make a mapping file for your lipid. The structure of the file is well described in [TA Wassenaar, et al. JCTC, 10:676-690, 2014] (and in the backward tutorial, I believe). Once you think you've create a good mapping file, just test it by running backward with that mapping file. If it works, i.e., the script does not crash and you get a nice backmapped configuration, you are good. If you have some more specific question feel free to post it here.
Last edit: 6 years 1 month ago by riccardo.

Please Log in or Create an account to join the conversation.

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
6 years 1 month ago #7546 by almeida
Replied by almeida on topic Mapping DPC with backward.py
DONE!

I followed the instruction in TA Wassenaar, et al. JCTC, 10:676-690, 2014, and this is the mapping file. I used the gromos .itp file for DPC from ATB database.
Thanks for the help.
; Modified from DMPC by Yasser Almeida Hernandez
; 2018-02-20

[ molecule ]
DPC

[ martini ]
NC3 PO4 C1A C2A C3A
;NC3-PO4-C1A-C2A-C3A

[ mapping ]
gromos  gromos43a1 gromos43a2 gromos45a3 gromos45a4 gromos53a5 gromos53a6 gromos54a7 

[ atoms ]
; Terminal head group (choline)
    1    C6   NC3
    2    C5    
    3    C4    
    4    N1    
    5    C8   NC3 NC3 PO4
    6    C7   NC3 PO4
; Phosphate group 
    7   O4P   PO4 PO4 NC3
    8    P1   PO4
    9   O1P   
   10   O2P   
   11   O3P   PO4 PO4 C1A
; Diacylglycerol  
   17    C1   PO4 C1A
   18    C2   C1A 
   19    C3    
   20   C15    
   21   C16   C2A 
   22   C17    
   23   C18    
   24   C19    
   25   C20   C3A
   26   C21   
   27   C22   
   28   C23      

;;;making a choline group
[out]
C5 N1 C6 C8
[chiral]
C4 N1 C6 C5 C8

Please Log in or Create an account to join the conversation.

Time to create page: 0.092 seconds