[gmx-users] parameters for bond types for GROMOS force field.

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 10 14:10:07 CEST 2012

On 6/10/12 8:03 AM, James Starlight wrote:
> Justin,
> thanks again for help.
> Finally is there any generall solution to parametrise hetero-groups covalently
> bonded with the protein ? Many proteins consist of such groups e.g chromophore
> in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes.

Parameterization schemes differ across force fields.  It's never easy.

> I've tried to make something like you've told me via inclusion of
> pre-parametrised residues in the existing gromacs ff but forced with some
> problems due to the atom order in new ITP and gro files provided by ATb or
> PRODRG are different from initial pdb file so pdb2gmx on the whole protein where
> het-group in the old order would not work properly :(

The output .itp files of ATB or PRODRG are not what you should be using.  You 
can't #include a covalently attached residue and expect the resulting dynamics 
to be relevant; it's not like a ligand.

What you need to do in those cases is create an .rtp entry (and any other 
incidental bonded and nonbonded additions, as stated before) that specifies 
whatever parameters you believe to be reliable.  At that point, when the .rtp 
file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it 
needs, it builds the topology.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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