AMBER Archive (2009)
Subject: Re: [AMBER] MM - PBSA problem
From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun Jan 25 2009 - 08:26:07 CST
On Sun, Jan 25, 2009, David A. Case wrote:
> Indeed, the mm_pbsa_createinput.pm module seems to be making a pbsa.in
> file that has cutcap, [xyz]cap in the &cntrl namelist. But none of
> these variables are in the pbsa code itself (in either Amber8 or Amber
> 10). If there is a developer who has time to look at this, that would
> be great.
> [The presence of cutcap,etc in the &cntrl namelist dates from CVS update
> 9.1 to mm_pbsa_createinput.pm, by Holger; since these variables really
> come from the prmtop file, they can probably just be removed from the
Just a extra note here: cutcap, xcap, etc. *are* in the &cntrl namelist
for sander, but not for pbsa. I don't know which program mm_pbsa is
calling with this input.
Bottom line: the original error may have a very different origin than
the one I suggested.
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