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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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