.IFN file in ATB server

hello
ATB server provides an item called .IFN file. how this parameters can be used to be added to the Gromos96 force field?

Why do you need that file? Doesn’t ATB provide everything in GROMACS format? The .ifn file is for use in GROMOS, so in principle its contents could be translated but the question is why you think you need to do that.

actually my protein includes both Cu and Zn. I have to work with Gromos FF so that they are recognizable. it seems that only Gromos96 43a7 is compatible with ATB output since when I try Gromos96 43a1, the atom names are quiet different and gives the relevant error. The point is Gromos96 43a7 cant recognize Zn atom.
Thank You dear Justin
-Sara

All of the force fields already built into GROMACS support Zn2+ (note: important distinction as this is not an atom, it is an ion and I suspect that’s what you’re dealing with in a biological system). The challenge is Cu2+, which is relatively uncommon in biomolecular force fields because transition metal parameters are generally pretty rough. Porting in a single atom type is relatively straightforward, a simple matter of converting the format and adding it to the .atp and .rtp files (if you need pdb2gmx to recognize it) and ffnonbonded.itp.

I have no idea of the quality of anyone’s Cu2+ parameters, but be very skeptical and assess interactions with proteins very carefully. Parameters exist for CHARMM that yield a very good hydration free energy but again, no one has looked at their applicability to protein systems, AFAIK.

I will take your explanations. I hope it works. Thank you for your consideration.
-Sara