On Apr 6, 2012, at 10:33 PM, Acoot Brett <acootbrett.yahoo.com> wrote:
> "it" means a paragraph of the Amber tutorial, or from a previous AMBER mail list.
>
> Suppose leap can automatically gives the correct protonation state of "HIS" with input as the "H" removed PDB file, can someone introduce the possible diffence of the protonation state made by this step in comparison with the HIS protonation state given by REDUCE?
Leap adds hydrogens based on which hydrogens are present in the library file for that particular 3-letter codon. For instance, HIE and HIS are the same and are singly-protonated at the epsilon position. HID is singly-protonated at the delta position, and HIP is doubly-protonated.
You need to specify which protonation state you want by setting the residue name to the appropriate 3-letter name in the PDB file.
If unexpected hydrogen atoms are there, you will get an error.
> In fact, the situation should be much complex. As for even for predetermined protonation state HIS, the protonation state could be changed during the MD process.
This was part of the motivation behind constant pH MD, which is implemented in sander -- it is described in the free energy chapter of the Amber manual.
This method allows the protonation state of titratable residues to change during the simulation while maintaining a thermodynamically meaningful ensemble.
The manual and original paper by Mongan et al. has more information here.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 07 2012 - 00:00:04 PDT
