Hello,
Step 2 of the Constant pH tutorial points out the residue names:
http://ambermd.org/tutorials/advanced/tutorial18/section1.htm
"Modify the residue names of the residues you wish to titrate, making
the following substitutions (the reference pKas shown are for the
capped, neutral amino acid in solution):"
Also, the manual tells us that LYS, TYR and CYS residue names are not
changed (pg. 162 of the Amber12 manual).
Hope this helps.
-Christina
On Thu, Jul 11, 2013 at 8:46 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> How do I do so.? Coz I don't know what residue names should I change to for the basic residues.
>
> Sent from my iPhone
>
> On 11 Jul, 2013, at 8:46 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>>
>>
>> On Jul 11, 2013, at 3:58 AM, "#YIP YEW MUN#" <YIPY0005.e.ntu.edu.sg> wrote:
>>
>>> Hi,
>>>
>>> Is it possible to do constant pH simulations by titrating the basic
>>> residues as well?
>>
>> Yes.
>>
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
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--
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Christina Bergonzo, PhD
Postdoctoral Fellow
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Office: Biopolymers Room 295
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Thu Jul 11 2013 - 08:30:02 PDT
