AMBER: Re: amber-developers: -y option in sander

From: Geoff Wood <>
Date: Thu, 19 Jul 2007 15:54:47 +0200

Dear Amber developers

I was wondering what the latest is on this problem? I am in need of
a working version too.



From: Gustavo Seabra <>
Date: Mon Mar 05 2007 - 20:48:06 GMT

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
> unrelated bug that needs to be fixed. Basically things don't work
> 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-
> 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]
>> 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
>> 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 7 06:07:27 2007

Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
BCH 4108
CH - 1015 Lausanne

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Received on Sun Jul 22 2007 - 06:07:32 PDT
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