Re: Reg: Solvation box

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Sun Jun 02 2019 - 08:18:33 CDT

Thanks a lot.

On Sun, Jun 2, 2019 at 6:43 PM Pratik Narain Srivastava <
pratik.narain_at_gmail.com> wrote:

> Yes you can. The role of a buffer in case of a protein molecule is mostly
> to maintain correct protonation states of its residue side chains. At
> physiological pH, protonation of His side chains appear to be most
> important. We use the H++ server to assign protonation states to our
> systems before simulating them in water. I suggest you try the same.
>
> On Sun, 2 Jun, 2019, 6:38 PM Adupa Vasista, <adupavasista_at_gmail.com>
> wrote:
>
>> But will that effect my interactions with protein.
>>
>> I need to do simulation on Amyloid beta aggregate under physiological
>> conditions. in experiments they recreated the physiological conditions
>> using Phosphate buffer such that it maintains pH of 7.4
>>
>> Can I safely use water?
>>
>>
>>
>> On Sun, Jun 2, 2019 at 5:12 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>>>
>>>
>>> On Sun, Jun 2, 2019 at 4:55 AM Adupa Vasista <adupavasista_at_gmail.com>
>>> wrote:
>>>
>>>> I need to have phosphate buffer with pH 7.4 as solvent in my simulation
>>>> .Is it possible?
>>>>
>>>
>>> just use plain water.
>>>
>>>>
>>>> Thank you
>>>>
>>>> --
>>>>
>>>> *A.VasistaM.Tech,Department Of Chemical Engineering,*
>>>> *IIT Guwahati.*
>>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>
>>
>> --
>>
>> *A.VasistaM.Tech,Department Of Chemical Engineering,*
>> *IIT Guwahati.*
>>
>

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*

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