Re: Reg: Solvation box

From: Pratik Narain Srivastava (pratik.narain_at_gmail.com)
Date: Sun Jun 02 2019 - 08:13:06 CDT

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.*
>

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