# Residue 'DOP' not found in residue topology database **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, mdp-parameters, mdrun, simulation-setup\ **Created:** [April 29, 2024, 11:08am UTC](https://gromacs.bioexcel.eu/t/residue-dop-not-found-in-residue-topology-database/9018 "2024-04-29T11:08:14Z")\ **Posts on this page:** 5\ **Page:** 2
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [May 6, 2024, 9:01pm UTC](https://gromacs.bioexcel.eu/t/residue-dop-not-found-in-residue-topology-database/9018/21 "2024-05-06T21:01:43Z")
Look, DOPC means dioleoyl (DO) phosphatidylcholine (PC). By definition, oleic acid has C18 and a double bond, so if your lipid is saturated and C10/C8, it cannot be DOPC. It will be caproyl-capryloyl-phosphatidylcholine, or the other way around, depending on the order of bonds to glycerol - either way, it’s quite uncommon, so not sure if it has a specific abbreviation. But ok, nomenclature aside. Again, what you’re asking is quite non-trivial and requires a good grasp of how molecule topologies work. In your case, I’d go with Packmol, and start by creating the lipid topology/structure of the C12/C12 glycolipid through Glycan builder, and just getting a single C12/C12 phospholipid through membrane builder or whatever it takes. Then, again, use the [said Gromologist functions](https://gitlab.com/KomBioMol/gromologist#adding-and-removing-atoms-while-maintaining-ordered-numbering) to remove the excess atoms from the end of the tail in both cases, and edit terminal types/charges to make sure you end up with a -CH3 end. Do the same with the structures. Run both through `gmx grompp` to make sure there are no errors in the topologies. Once you have the topologies of both components, use Packmol to produce a bilayer, and combine the topologies to account for the correct numbers of lipids. Then you’ll have to proceed with the standard equilibration etc. to make sure your bilayer is stable over at least 10-50 nanoseconds. As you see, it’s doable but definitely non-standard, so expect quite a few setbacks during the process. It’s a good learning opportunity though. ---
**Author:** ![Fayaz](https://avatars.discourse-cdn.com/v4/letter/f/22d042/32.png) [@Fayaz](https://gromacs.bioexcel.eu/u/Fayaz)\ **Post date:** [May 11, 2024, 6:00am UTC](https://gromacs.bioexcel.eu/t/residue-dop-not-found-in-residue-topology-database/9018/22 "2024-05-11T06:00:57Z")
1,2-dioctanoyl-sn-glycero-3-phosphocholine is my molecules here look at tails is C10C8. Couldn’t be available in charm gui ---
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [May 11, 2024, 10:53am UTC](https://gromacs.bioexcel.eu/t/residue-dop-not-found-in-residue-topology-database/9018/23 "2024-05-11T10:53:54Z")
1,2-dioctanoyl means two C8 chains, not C10C8 (by which I understand C10 at position 1 and C8 at position 2). Please double-check which version is true. ---
**Author:** ![Fayaz](https://avatars.discourse-cdn.com/v4/letter/f/22d042/32.png) [@Fayaz](https://gromacs.bioexcel.eu/u/Fayaz)\ **Post date:** [May 11, 2024, 1:21pm UTC](https://gromacs.bioexcel.eu/t/residue-dop-not-found-in-residue-topology-database/9018/24 "2024-05-11T13:21:21Z")
Yes but this is not available in charmm GUI. Can you please tell me further? ---
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [May 11, 2024, 2:26pm UTC](https://gromacs.bioexcel.eu/t/residue-dop-not-found-in-residue-topology-database/9018/25 "2024-05-11T14:26:09Z")
I outlined the whole process in the message 5 days ago. Still, your first step is knowing which lipid you want to simulate. [Previous page](https://gromacs.bioexcel.eu/t/residue-dop-not-found-in-residue-topology-database/9018.md?page=1)