On 11/06/2012 6:12 PM, James Starlight wrote:
Justin
1) So if I understood correctly I can make parametrisation of my
uncommon group by the atb for instance. Than I can change itp file to
rtp form and integrate this new residue to the existing ff. Finally
when I will run pdb2gmx on the protein with the same group (even with
different atom order) I obtain proper topology.top file. Doest it
correct ?
The "change" to which you refer will be non-trivial because of the
covalent bond. Charge distribution and atom types will change.
2) I've defined bond between both of my atoms as the gb_15 and define
this atoms as the C in the topology.top. Than I've run minimisation
and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form
and were not in the planar form :( What else should I do ? Could some
operations with the angle term in topology.top help me? I've modified
612 613 614 2 as the ga_27 but it also could not help me.
It is possible to hack something that will work, but the transferability
of charges from an isolated form to a form covalently bound to a peptide
is (at best) doubtful. If your atomic arrangement is changing, the
presence of single vs double bonds must be changing, and that should
basically guarantee non-transferability.
The most correct form of a solution is to parameterise the modified form
of the residue along the same lines as the original force field
parameterization. That may or may not be feasible for you. It's hard to
be more specific without knowing exactly what modified residue you are
seeking to create.
Mark
James
2012/6/10 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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