AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Fri May 30 2008 - 09:32:27 CDT

Thanks Bob,

Then I think I will give it a try with sander. Fingers crossed!
But are you sure that pmemd does not support mm_pbsa? Because according
to the mmpbsa tutorial, it should work
http://amber.scripps.edu/tutorials/advanced/tutorial3/section2.htm.

Cristina

Robert Duke wrote:
> The primary advantage pmemd offers is purely speed; there are a few
> minor convenience tweaks here and there, but it is mostly supposed to
> do a subset of sander functionality, not the other way around. So
> there should never be a problem moving back to sander from pmemd, as a
> general rule. Also note that pmemd does not support energy
> decomposition through the idecomp switch, and therefore does not
> support mm_pbsa anyway.
> Regards - Bob Duke
>
> ----- Original Message ----- From: "Cristina Sisu" <csds2_at_cam.ac.uk>
> To: <amber_at_scripps.edu>
> Sent: Friday, May 30, 2008 9:47 AM
> Subject: AMBER: Sander instead of PMEMD
>
>
>> Dear Ambers,
>>
>> I have a problem running PMEMD on our cluster. As far as I understand it
>> does not seem to be a program problem but rather the way that our
>> cluster is build (on module, environments, etc.). I want to do some
>> MMPBSA calculations on a protein-peptide ligand complex. Can I use for
>> the production run, Sander instead of the PMEMD? With the periodic
>> boundary condition parameter switched on, and using the same input (.in)
>> file as for PMEMD?
>> Would the trajectory obtained in this way be suitable for extracting
>> snapshots necessary for mmpbsa ?
>>
>> Thanks,
>> Cristina
>>

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