Hi,
On Fri, 27 Feb 2004, xiaolin cheng wrote:
>
> i'm using xleap in amber8 to create a "pertubation" prmtop file for free
> energy calculation.
> when I pull down the edit menu, there is column called DELTA.charge.
> my question is, what should I put in there?
> is it the "perturbed" charge minus original charge or something else?
>
> xiaolin
doc/leap.me, which has presumably been thoroughly proof-read, does
indicate
that definition:
The \fCpertCharge\fR property is a NUMBER. In spite of its name, it
actually
represents the \fIdifference\fR between the perturbed charge and the
regular
charge on an ATOM. Hence, if this value is zero (its default value), then
the
perturbed charge is the same as its regular charge. (Note that the
meaning of
this property is changed from Amber versions prior to 8. If you have OFF
files
with perturbed charges in them from earlier versions, you will need to
edit
these to the new standard--either use a text editor or the edit table in
xleap.)
Scott
ps.
previous bug reports on xleap are slowly being fixed:
Jim's move crash is fixed
Other similar problems in the code have been bullet proofed
Francois's addions is next
then Yong's Hxyz crash
Received on Wed Apr 05 2006 - 23:50:05 PDT
