I would suggest that you do your equilibration using restraints based on
your NMR data, not based on the original model that also included
supposition. do the equilibration including the NMR data, and then slowly
turn that off (or keep it, if you desire).
On Wed, Dec 16, 2015 at 9:07 AM, Trang Nguyen <trangnt.iastate.edu> wrote:
> Hi Amber-developers/users,
>
> Our group currently works with Enzyme I-PTS (monomer, 313aa) and ligand PEP
> (12atoms, -3 charge). The original model EI-PEP comes from our both
> supposition and NMR experiments. After running MD simulation for 1ns, we
> recognized that the ligand's structure has been changed significantly from
> the original structure (see attached file). To our point of view, this
> change in ligand's structure should not be acceptable, compared with the
> experimental model. Especially in case the change is caused mainly by
> solving bad contacts during system preparation. Now, we are working on
> different reasons causing the problem.
>
> - Sets of charge on ligand. We tried with different charge methods to see
> which performs better during simulations. We tried to get RESP charges with
> GAMESS-US output but failed. We are not sure that the providing script (of
> Dr Hans De Winter) works for GAMESS-US or PC-GAMESS. We also would like to
> try with R.E.D. server at http://q4md-forcefieldtools.org/REDS/ but it
> requires name and password for authorization.
>
> - Angle/bond/dihedral definition. It seems that we have to define our own
> lib and frcmod files for ligand. Then the ligand's structure after 1ns
> looks better (not changed so much with the experimental model). But could
> you please help me to check these parameters (please see the attached files
> for pdb, lib as "log" and frcmod)
>
> - The final thing are parameters when running MD simulation from
> minimization to production. We did minimize system with strong restraint on
> both protein and ligand (at the first time, by following some online
> tutorials, we only restraint backbone of protein), then minimize with soft
> restraint and fully relax. For heating, density and equilibrium, we also
> tried to perform the same thing: strong restraint then relax gradually.
> Btw, can we perform restraint with different forces for different groups?
> i.e. strongly restraint on ligand, and weakly restraint on backbone.
>
> Could you please give me any suggestion. Do these approaches sound
> reasonable to get through the problem.
>
> Thank you very much
>
> Best Regards,
> Trang Nguyen
>
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Received on Wed Dec 16 2015 - 06:30:06 PST
