AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA help, please

From: opitz_at_che.udel.edu
Date: Mon Jul 11 2005 - 16:15:19 CDT

('binary' encoding is not supported, stored as-is) Thank you! That did fix the problem. I have run into another problem. It
appears that I need to implement Bugfix 7 for Amber 7.
I'm fairly unexperienced with programming, so is it correct that I have
to go into the mdread.f file and change the lines by hand?

Best Regards,

Armin

==============Original message text===============
On Mon, 11 Jul 2005 14:30:34 EDT Scott Pendley wrote:

Armin,

I have seen that error when mm_pbsa is try to process snapshots and
there are none available. As GC is marked zero, it assumes that you
are not creating individual snapshots from a given trajectories. Is
this what you wish to do?

SURFTEN and SURFOFF are specific to the type of GB or PB that you are
trying to perform. For a good referrence on this and mm_pbsa in
general see "Converging Free Energy Estimates: MM-PB(GB)SA Studies on
the Protein-Protein Complex Ras-Raf" Gohlke and Case. J Comput Chem
25:238-250 2004

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