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
>
>
>_______________________________________________
>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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 06 2012 - 19:30:03 PDT
