You can use periodic boundary with PB, though the solver is slow in Amber 12. The upcoming AmberTools should have a faster solver. This is not for MD, but for mmpbsa calculations only. As usual you may need to use PBSA directly for unusual input options.
Ray Luo, Ph.D.
On Apr 8, 2013, at 9:17 AM, Syed Tarique Moin <tarisyed.yahoo.com> wrote:
> Hello, Hai,
>
> Actually I want to get a complex conformation with an unknown binding pattern with this method which is faster.
>
> Thanks
>
> Tarique
>
>
>> ________________________________
>> From: Nhai <nhai.qn.gmail.com>
>> To: Syed Tarique Moin <tarisyed.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>> Sent: Monday, April 8, 2013 5:50 PM
>> Subject: Re: [AMBER] implicit solvation with periodic boundary
>>
>> What do you want to learn/get from this kind of simulation?
>>
>> Hai
>>
>> On Apr 8, 2013, at 11:39 AM, Syed Tarique Moin <tarisyed.yahoo.com> wrote:
>>
>>> Hello,
>>>
>>> I am interested to simulate a protein in implicit solvent with periodic boundary condition. Can someone suggest me is it possible in Amber.
>>>
>>> Thanks
>>> Tarique
>>>
>>>
>>> -----------------------------------------------------------
>>>
>>> Syed Tarique Moin, Ph.D.
>>> Post Doctoral Fellow,
>>>
>>> Institute of General, Inorganic and Theoretical Chemistry
>>> Center for Chemistry and Biomedicine
>>> University of Innsbruck
>>> Innrain 80-82
>>> A-6020 Innsbruck
>>> AUSTRIA, Europe
>>> _______________________________________________
>>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 08 2013 - 10:00:03 PDT
