amber-developers: -y option in sander

From: David A. Case <>
Date: Mon, 5 Mar 2007 12:10:53 -0800

we have a version and planned to patch the code but it revealed another
unrelated bug that needs to be fixed. Basically things don't work well
for PBC. I need to get that info to Mike Crowley and will do so after
a grant deadline this week. I can give you working code for non-periodic.

On 3/1/07, Gustavo Seabra <> wrote:
> That option is listed on Amber 9 manual, but whenever I try to use it, i
> get:
> > sander -O -i mdin -o mdout -y reaction.crd
> mdfil: Error unknown flag: -y
> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
> -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
> mdinfo -radii radii]
> Consult the manual for additional options.
> Was it removed from sander for some reason? Or has it never really
> worked? I am sending this to the developer's list because, since it is
> in Amber 9's manual, I assume it has been removed in Amber 10. If so, is
> there a reason for it? Is there a replacement? (I was actually planning
> to use that...)
> Thanks,
> Gustavo.

[Carlos: please send mail to, with "subscribe
amber-developers" in the body of the message....thx.]
Received on Wed Mar 07 2007 - 06:07:27 PST
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