AMBER Archive (2003)

Subject: Re: MM_pbsa prmtop file

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 09 2003 - 17:53:53 CST

On Thu, Jan 09, 2003, wentaofu wrote:
>
> I plan to use some old MD simulation results on Amber6.0 and do MM_pbsa
> calculation on amber7.0. The message I got from Amber7.0 is
>
> " GB calculations now require a new-style prmtop file"
>
> Would you please let me know what should I do? I don't plan to run the MD
> simulation again. Is it possible to just generate the new-style prmtop file
> and do the MM_pbsa using the current MD trajector file?
>

Yes, this is what you would need to do.

> Is there any
> infulence on the amber7.0 MM_pbsa calculation results by using of amber6.0 MD
> simulation results.
>

There should not be. Amber 6 and Amber 7 give identical results for the
usual sorts of solvated simulations with PME, and the format of the trajectory
files have not changed.

..good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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