Explaination of ff parameter abbreviations!

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Hi,

I want to understand gmx ff parameters written in the abbreviations attached below. Can someone provide me some link explaining each of these short forms and what does these values refer to. Also how can i calculate these values from available PDB/Sdf files?

defaults

nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ

atomtypes

name at.num mass charge ptype sigma epsilon sigma_14 epsilon_14

bondtypes

i j func b0 Kb

angletypes

i j k func th0 cth S0 Kub

dihedraltypes

i j k l func phi0 cp mult

2

The manual explains all of these items. They have no relation to coordinate files like PDB.

3

Found it Dr.

I have a related query. I was trying to add a ligand In opls ff. But there’s no entry for atomtypes in ffbonded. Where should I make the entries of new atomtypes. For other bond types: pair types I will have to modify ffbonded and ffnonbonded for dihedrals I guess but, where to define atomtype entries? I want to use opls for membrane protein ligand simulations.

4

Atom types are defined in ffnonbonded.itp.