[gmx-users] Unit of force constants and adding new residue.

[Dawid das]

Dear Gromacs experts,

I have a few questions regarding adding a new residue to the force field.

1) In what unit should provide force constants for stretching, bending and
torsion in aminoacids.rtp file? I can't really figure that out from gromacs
manual.

2) If I provide those constants and natural values of bond lengths, angles,
etc.  in aminoacids.rtp file, do I need to provide them in ffbonded.itp?

3) My new residue has to be connected with two natural aminoacids (Phe,
Gly, etc.). Where do I specify the parameters for new atom types (of my
new  residue) and for these "regular" atom types? For example, torsion or
stretching paramters where those two residues are connected.

What I want to do exactly is to add parameters from Tinker format FF for a
chromophore of mCherry fluorescent protein. I try to do things according to
this manual:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

I will be grateful for any help :).

Best wishes,
Dawid Grabarek