search

piskuliche / itp2moltemplate

Python script for converting Martini ITP files to moltemplate force field files.
3 stars 0 forks source link

Hints for starting itp2moltemplate #1

Open kleflick opened 2 years ago

kleflick commented 2 years ago

hi, I need some hints to use your program. What are the three files I have to use for starting the conversion? I have tried some different combinations but without success. Thank you Klemens

piskuliche commented 2 years ago

Hi Klemens,

This code is still in development and I haven't gone through and really formatted the code for outside use yet - but it does work. The code is run as martini2moltemplate.py [force field name] [molecule name] [.gro file]

The force field name argument just names the output moltemplate forcefield file. The molecule name argument needs to match what is found in one of the itp files, and the gro file should match what can be found on the Martini website. Note that this code only works for lipids and has only been extensively tested on the Dry Martini model.

Other files you need:

! These all can be downloaded from the MARTINI website Dry-Martini/dry_martini_v2.1.itp Dry-Martini/dry_martini_v2.1_lipids.itp Dry-Martini/dry_martini_v2.1_solvents.itp Dry-Martini/dry_martini_v2.1_cholesterol.itp Dry-Martini/dry_martini_v2.1_ions.itp ! This is one I made for my own use and didn't download, you can just delete the line near the bottom where this shows up. Dry-Martini/addmol.itp

You theoretically should be able to switch the lines that call for the itp files to wet MARTINI and have it still work, but I've only tested that to a small extent.

I hope this helps! Zeke