# INSANE not compatible with martini3 GM3? **URL:** \ **Category:** User discussions\ **Tags:** forcefield, simulation-setup\ **Created:** [November 27, 2025, 12:30pm UTC](https://gromacs.bioexcel.eu/t/insane-not-compatible-with-martini3-gm3/12979 "2025-11-27T12:30:46Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Luke\_M](https://avatars.discourse-cdn.com/v4/letter/l/77aa72/32.png) [@Luke\_M](https://gromacs.bioexcel.eu/u/Luke_M)\ **Post date:** [November 27, 2025, 12:30pm UTC](https://gromacs.bioexcel.eu/t/insane-not-compatible-with-martini3-gm3/12979/1 "2025-11-27T12:30:46Z")
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](https://mad.ibcp.fr/molecule/DPG3?version=838991444671996362) 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. ---
**Author:** ![Luke\_M](https://avatars.discourse-cdn.com/v4/letter/l/77aa72/32.png) [@Luke\_M](https://gromacs.bioexcel.eu/u/Luke_M)\ **Post date:** [December 1, 2025, 11:55pm UTC](https://gromacs.bioexcel.eu/t/insane-not-compatible-with-martini3-gm3/12979/2 "2025-12-01T23:55:43Z")
As a workaround I have used insane to build the pdb and a script to manually add in the virtual site atoms afterwards.