"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?
If we do not remove H for leap input and we select to modify the protonation state based on REDUCE prediction (or some other prediction), should we correspondingly change the 3-letter codon of HIS in the PDB file, or we still keep the codon as "HIS" for all different states of HIS protonation, and then we input the PDB file to leap and we leave leap for the 3-codon modification?
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.
Thus does anyone has the experience to show the influence of HIS protonation on the MD results of a protein?
Cheers,
Acoot
________________________________
From: Dean Cuebas <deancuebas.missouristate.edu>
To: Acoot Brett <acootbrett.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, 7 April 2012 12:16 PM
Subject: Re: [AMBER] question on protonation state of histidine
What is "it"?
Cheers,
Dean
On 4/6/12 5:48 PM, "Acoot Brett" <acootbrett.yahoo.com> wrote:
>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
>
>
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Received on Fri Apr 06 2012 - 20:00:03 PDT
