Dne Thu, 12 Feb 2015 23:44:14 +0100 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> There might be a misunderstanding here. MMPBSA.py only minimizes the
> snapshots before running normal mode analysis. The problem is if you
> run minimization in sander, then do the MM/GBSA or MM/PBSA part (not the
> normal mode part). For normal modes, it’s fine, but you can’t use the
> same trajectory for normal modes AND GBSA/PBSA.
Don't worry I would never use minimized frames for GBSA/PBSA part :)) From
the start I was discussing just normal mode part of the MM/PBSA analysis.
> If more are omitted, that’s bad, for sure. But the low-frequency modes
> (like mode 7) may still change >when the convergence criteria is
> tightened. It’s worth comparing if you’ve done both calculations.
Please see the attached output files from my test case drms 1e-6 vs drms
1e-2.
Also the low frequency (7,8,9 ..) are pretty similar for both cases.
But as I wrote I will try the same experiment for bigger systems.
Best wishes,
Marek
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 12 2015 - 15:30:02 PST
