No default improper dihedral types in Amber ff14sb-OL21 for DNA simulations

TGaziri
Sat, 14 Dec 2024 00:08:04 +0000
User discussions

GROMACS version: 2022.4
GROMACS modification: No

Hello,

I’m trying to set up a DNA simulation with Amber OL21, using the Gromacs port of the ff14sb-OL21 forcefield. But after I created the topology I got a bunch of the same error for different improper dihedrals when I try to run gmx grompp:

ERROR 1 [file topol.top, line 705]:
  No default Improper Dih. types

But the weird part is that when I checked some of the dihedrals they’re defined on the ffbonded.itp file of the forcefield. and others even if you try to defined them they don’t work

For example atoms 9 11 12 23. (CT - N* - CM - C).
This dihedral exists in the ffbonded:

C CM N* CT 4 180.00 4.18400 2

But It still gives the same error, I have tried even copying and pasting this dihedral with the same atom order as it’s on the topology, but it doesn’t fix the errors.

If I try adding an improper dihedral that doesn’t seem to exist in the ffbonded.itp file, it simply doesn’t work even though the formatting is correct. I have done it multiple times with other forcefields.

If I were to change the function type 4 (which is supposed to be used for improper dihedrals) to 2 it reduces the number of errors but creates a new error

ERROR 1 [file ffbonded.itp, line 847]:
  Too many parameters or not enough parameters for topology B

I’m really on a dead end right now, I’m only using the amber forcefield because it was supposed to be better for DNA.

All my pertinent files can be found in this link:

MD-FIles for DNA simulation with amber

Any help will be appreciated,

Thank you

3 posts - 2 participants