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Mapping DPC with backward.py
- almeida
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6 years 2 months 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
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
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- riccardo
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6 years 2 months ago - 6 years 2 months 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 2 months ago by riccardo.
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- almeida
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6 years 2 months 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.
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
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