Re: Reg: Solvation box

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Tue Jun 04 2019 - 01:37:20 CDT

sorry that is PROPKA.

Thank you

On Sun, Jun 2, 2019 at 7:18 PM Adupa Vasista <adupavasista_at_gmail.com> wrote:

> Its easy to get the pdb file from H++ or Pokra and continue the simulation
> with plain water as said by pratik.
>
> Thank you
>
> On Sun, Jun 2, 2019 at 6:58 PM Jim Parker <jimparker96313_at_gmail.com>
> wrote:
>
>> Adupa,
>> Perhaps this would help. Think about what pH 7.4 means. approximately
>> 1 in 10^7 water molecules are split into a H+ and OH- units. How many
>> water molecules are in your simulation? 10K, 100K, 1M? If so, you would
>> not see a difference between plain water and the pH 7.4 solution.
>> Depending upon the molarity of your buffer, you might also add some
>> phosphate ions to your simulation. But again, think about the size of your
>> computational region to determine if that generates a reasonable
>> concentration of buffer.
>>
>> As recommended by Pratik, the protonation state of the protein is the
>> feature that reflects the change in your environmental conditions.
>>
>> On Sun, Jun 2, 2019 at 8:08 AM 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.*
>

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

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