Re: amber-developers: -y option in sander

From: Gustavo Seabra <>
Date: Mon, 05 Mar 2007 15:48:06 -0500

Thanks Dave and Carlos,

I can wait, there's no hurry. I'll remember to ask for that code if I
need it earlier.



David A. Case wrote:
> Gustavo,
> 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.
> Carlos
> 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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