Thank you Bill
George
On Jul 29, 2011, at 5:09 PM, Bill Miller III wrote:
> I have never tried running MMPBSA.py with ptraj-generated cluster
> trajectories, but I don't see any reason that won't work.
>
> -Bill
>
> On Fri, Jul 29, 2011 at 10:58 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Thank you Bill,
>>
>> ptraj cluster generates cluster trajectories. I assume that I should run
>> these trajectories through MMPBSA.py using new prmtop files for protein,
>> ligand and complex
>>
>> Cheers
>>
>> George
>>
>>
>> On Jul 29, 2011, at 3:56 PM, Bill Miller III wrote:
>>
>>> You could combine all the coordinate frames for each cluster into their
>> own
>>> "trajectory" using ptraj and run each of those trajectories through
>>> MMPBSA.py.
>>>
>>> I hope that helps.
>>>
>>> -Bill
>>>
>>> On Fri, Jul 29, 2011 at 9:21 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>>
>>>> I've conducted a 16ns MD production simulation of a protein-ligand
>> complex.
>>>> I've obtained the delta G energy of the complex using MMPBSA.py. I've
>> also
>>>> obtained clusters of coordinate frames from the trajectory.
>>>>
>>>> My question is whether there's a way of obtaining the delta Gs of these
>>>> clusters.
>>>>
>>>> Thanks in advance for any advice
>>>>
>>>> George
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Bill Miller III
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Graduate Student
>>> 352-392-6715
>>> _______________________________________________
>>> 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
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> 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 Fri Jul 29 2011 - 09:00:05 PDT
