GROMACS version: 2020.2
I have encountered the following error when trying to write a tpr file using the ff14sb AMBER force field: ERROR 6 [file topol_Protein_chain_B.itp, line 142001]: No default Improper Dih. types. I have seen that ffbonded.itp may have to be edited. Are there any other approaches/any explanations for why I may be receiving this error?
Where did you get ff14SB force field files? Whoever produced them may not have done a very thorough job of validating them, so be skeptical of their quality. Missing a parameter in a protein is a pretty massive oversight.
Okay, I see. The files are from: https://fch.upol.cz/ff_ol/gromacs.php . Is there somewhere else that they should be sourced from?
No idea, but it looks like they took a user contribution off of gromacs.org and there’s no guarantee that those files are correct. They appear to have done validation, but the question really is: what is the missing parameter? Some corner case they might have missed, something weird like a Gly-Pro linkage that got overlooked?
I have come across the following, but I am a bit unsure of this approach. Further thoughts?: http://zhenglz.blogspot.com/2017/05/fixing-bugs-in-ff14sb-port-for-gromacs.html
Compare the values against the original AMBER force field files and if they match (after unit conversion), then that’s an appropriate fix. Really anyone distributing a force field port should also be doing validation to avoid such problems.
Do you happen to have a source for the ff14sb files? I cannot seem to download them. If so, that would be great. Also, I am unsure where there would need to be a conversion exactly. Thank you for all of your help.
You can get the force field files with the (free) AmberTools package.
Got them, thank you for all of your help.
I followed the Fixing bugs in FF14SB port for Gromacs and can fix the “No default Improper Dih. types” error.
I downloaded the amber14sb_parmbsc1.ff.tar.gz
from Force fields - Gromacs and needed to edit by adding on more line
NA CV CC CT 4 180.00 4.60240 2
at line 783
to the amber14sb_parmbsc1.ff/ffbonded.itp.
Then, it works!
This worked perfectly, thank you!