Mikkel Dahl Andreasen

icon indicating a website link https://chem.au.dk/en/research/research-areas-and-groups/theoreticalchemistry/biomodelling

icon company Aarhus University, Department of Chemistry icon location PhD student in the Biomodelling group at the Department of Chemistry at Aarhus University

Results 14 comments of Mikkel Dahl Andreasen

Problems with -nt -cter and -nter when Martinizing from Charmm36 to M3

### Reply to pckroon **The file "LOG_martinize2_COOHter" contains the martinize2 output with "-cter COOH-ter". Full command shown below (it created the same warning as the other "-cter" and "-nter" flags...

Problems with HSE, HSP and ASPP when Martinizing from Charmm36 to M3

The standard pdb format uses column 18, 19 and 20 as the residue name, but quite a few forcefields also use column 21 for the residue name, and since column...

Use in PEGylated protein workflow of polyply

Hello Fabian I would very much be willing to help convert the commands from insane to CGSB. I assume it is only the commands in the tutorial that you linked....

Creating a bilayer with embedded small molecules

That should be simple enough to do. If it is just a single molecule (or only a few) you need placed inside the membrane, then you could insert it manually...

Creating a bilayer with embedded small molecules

Hello I think the error is caused by an outdated package. I am personally running with shapely v2.0.4. From what i can tell from their versions, this method of calling...

Creating a bilayer with embedded small molecules

Hello That is not possible in the current version (v1.0.0) as it just places all "lipids" (membrane components) as close to the center of the membrane as possible. I just...

Creating a bilayer with embedded small molecules

Hello COBY does not feature a way to affect the exact placement in the way you want. You can use "gm_ld:evenly", which makes the grid maker lipid distribution algorithm ensure...

Creating a bilayer with embedded small molecules

I don't think it is possible to get exactly the placement that you want with a single membrane since the pattern is not constant with equal distances between all RES....

Creating a bilayer with embedded small molecules

You could try to shift the pattern for one of the leaflets like shown below. ``` ### (POPC, RES) PR = (6, 3) P = (9, 0) ### Each represents...

Creating a bilayer with embedded small molecules

Hello. I don't know why it only corrects the placement for two of the rows. Could i get you to post your entire COBY command (including things calculated before the...