GROMACS version: 2023.3
GROMACS modification: No
Hi everyone, I am having an issue with setting up my membrane using INSANE.
I want to include the lipid GM3 (Monosialodihexosylganglioside) aka DPG3.
I am using martini3 and the most recent version of INSANE, and using the .itp file from MAD - MArtini Database - Database for coarse grained biomolecules
An issue arises as there seems to be a mismatch between the .itp file for GM3 and the glycolipid schematic in INSANE.
Here is the martini3 parameter file for GM3 / DPG3:
[ moleculetype ]
DPG3 1
[ atoms ]
1 SP1r 2 GLC A 8 0.0 54.0
2 SP1r 2 GLC B 9 0.0 54.0
3 SP1r 2 GLC C 10 0.0 54.0
4 TC4 2 GLC V 11 0.0 0.0
5 SN6 3 GAL A 12 0.0 54.0
6 SP4r 3 GAL B 13 0.0 54.0
7 SP1r 3 GAL C 14 0.0 54.0
8 TC4 3 GAL V 15 0.0 0.0
9 Q5n 4 NMC A 16 -1.0 72.0
10 SN6 4 NMC B 17 0.0 54.0
11 SP1r 4 NMC C 18 0.0 54.0
12 SP3d 4 NMC D 20 0.0 54.0
13 SP3 4 NMC E 21 0.0 54.0
14 TC4 4 NMC V 22 0.0 0.0
15 SP1 1 CER AM1 0 0.0 54.0
16 SP2 1 CER AM2 1 0.0 54.0
17 C4h 1 CER T1A 2 0.0 54.0
18 C1 1 CER C2A 3 0.0 54.0
19 C1 1 CER C3A 4 0.0 54.0
20 C1 1 CER C1B 5 0.0 54.0
21 C1 1 CER C2B 6 0.0 54.0
22 C1 1 CER C3B 7 0.0 54.0
23 C1 1 CER C4B 8 0.0 54.0
Highlighted in bold are 3 virtual sites included in the structure (the grey beads in the link to the 3d image), however the INSANE building schematic does not accommodate for these virtual sites:
[ glycolipids ]
; Prototopology for longer and branched glycosil and ceramide based glycolipids
;
; 17-15-14-16
; |/
; 13
; |
; 12-10-9-7-6-4-3-1–18–20-21-22-23-24-25
; |/ |/ |/ |/ |
; 11 8 5 2 19–26-27-28-29-30-31
As a comparison, here is SAP6 an inositol, that also contains a virtual site, but is accommodated in the INSANE building schematic:
[moleculetype]
; molname nrexcl
SAP6 1
[atoms]
; id type resnr residu atom cgnr charge (mass)
1 SP1 1 SAP6 C1 1 0
2 SP1 1 SAP6 C2 2 0
3 SP1 1 SAP6 C3 3 0
4 TC4 1 SAP6 C4 4 0 0 ; Massless virtual bead
5 Q5 1 SAP6 PO4 5 -1.0
6 D 1 SAP6 P4 6 -1.5
7 D 1 SAP6 P5 7 -1.5
8 SN4a 1 SAP6 GL1 8 0
9 SN4a 1 SAP6 GL2 9 0
10 SC1 1 SAP6 C1A 10 0
11 C5h 1 SAP6 D2A 11 0
12 C5h 1 SAP6 D3A 12 0
13 C4h 1 SAP6 D4A 13 0
14 C1 1 SAP6 C5A 14 0
15 C1 1 SAP6 C1B 15 0
16 C1 1 SAP6 C2B 16 0
17 C1 1 SAP6 C3B 17 0
18 C1 1 SAP6 C4B 18 0
[ inositollipids ]
; Template for phosphatidylinositol type lipids
; 1 2 3 4, is the inositol
; 5, is the phosphate that links to the tail part.
; 6 7 8 ,are potential phosphates
;
; 6
;
; 7-2–1-5-9–11-12-13-14-15-16
; |4/ |
; 8-3/ 10-17-18-19-20-21-22
;
Site 4 is the virtual site inside the ring structure, which is lacking in the glycolipid schematic.
Am I completely missing something or doing something wrong? Or is the martini3 GM3 .itp indeed not compatible with the current version of INSANE?
I have attempted to build the pdb without the virtual sites, as I have read that GROMACS can add them at the start of the simulation. However, I then get the basic fatal error that my pdb and itp/top have a mismatched number of atoms (as expected). I could simply remove the virtual sites from the itp, but this would of course change the officially released structure, which I do not want to do.
Thank you in advance for any advice or assistance.