Dear All,
But in order to prepare the AMBER input file, it suggest to remove all the H. Does this also makes the different protonation state of HIS undistinguishable in the intial step of AMBER for input file preparation? All the H removal process does not remove the protonation H of HIS?
Cheers,
Acoot
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Acoot Brett <acootbrett.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, 6 April 2012 11:28 PM
Subject: Re: [AMBER] Further question on protonation state of histidine
On Fri, Apr 06, 2012, Acoot Brett wrote:
>
> Even for high resolution structure of protein, the protonation state of
> HIS is usallly unclear or unspefified. Do we have some rules to correct
> the protonation state of the residues including HIS? Or there is a
> server for this purpose?
What leap does by default is determined by your leaprc file; all of the
standard leaprc files use HIE by default. But it is recommended that you
examine each residue and not rely on the default. The reduce program (now
included in AmberTools) can help, as can the "H++" program on the web. Other
tools for estimating protonation states exist--these are just the ones I am
most familiar with.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 06 2012 - 16:00:04 PDT
