Re: [AMBER] Assigning protonation o residues for parallel tempering

From: Daniel Sindhikara <>
Date: Wed, 10 Jul 2013 08:31:20 +0900

If you are asking whether protonation states affect PT/REMD simulations,
then yes.

If you want to manually change the protonation state, edit the PDB residue
to be HID or HIP according to whichever you think is the most appropriate
(and delete
any extra hydrogens if necessary). Then load the modified PDB into LEaP.


On Wed, Jul 10, 2013 at 2:04 AM, Francesco Pietra <>wrote:

> Hello:
> I am preparing files for parallel tempering to hopefully get a
> dominant cluster of conformations for the unstructure (X-ray diffr)
> tails of a protein homotrimer.
> A problem: Poissson-Boltzmann calculations of pKa assign diprotonation
> to most histidines of these tails (generated with MODELLER), except
> for one subunit, where one histidine is assigned HIE. The apparent
> reason is that this particular histidine comes closer (according to
> MODELLER) to two other tails, while the other histidines of these
> tails feel the bulk solvent. There is no reason that this represents a
> low-energy situation.
> I expect that parallel tempering is biased by the protonation assigned
> to any titrable group for cases as illustrated above.
> Grateful for advice.
> francesco pietra
> _______________________________________________
> AMBER mailing list

Dr. Daniel J. Sindhikara <>
Ritsumeikan University <> <>
AMBER mailing list
Received on Tue Jul 09 2013 - 17:00:03 PDT
Custom Search