Extra points are available in pmemd in amber 10. The implementation is
significantly faster than what is available in sander 9; if you are going to
use extra points much at all, it is probably worth upgrading to amber 10 so
you get extra points support in pmemd.
Regards - Bob Duke (the guy who did it)
----- Original Message -----
From: "mousumi" <mousumi.mmb.pcb.ub.es>
To: <amber.ambermd.org>
Sent: Wednesday, October 21, 2009 3:57 AM
Subject: [AMBER] "extra points" incompatibility with pmemd
Dear all,
I am trying to simulate a system containing DNA and ions using PMEMD. The
system has been solvated using the frcmod.tip4pew forcefield and TIP4PEWBOX
water box. After the normal minimization and equlibration with "sander"
when I am going for the MD production run, its giving me the error "PMEMD
cannot process prmtop files with extra points data! Please use sander 9.0
instead" and then stopped running. Please let me know what I should do to
avoid the error.
Thanks in advance,
Mousumi
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Received on Wed Oct 21 2009 - 05:30:02 PDT
