Re: AMBER: Amber 9, sander imin = 5, -y flag

From: Carlos Simmerling <>
Date: Mon, 01 May 2006 09:35:56 -0400

Dave Case is right, this will be addressed in a bug fix. for now use
"-x" for the
output trajectory.
carlos wrote:

>I am having problems with sander when imin = 5. Specifically, the -y (inptraj)
>flag isn't recognised. i.e.
> 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
>Consult the manual for additional options.
>The usage described in the manual is inconsistent with this in that the -y flag
>appears to be supported.
>Is this a bug or just an error of mine?
>Francis Peters
>University of NSW
>Sydney, Australia
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed May 03 2006 - 06:07:07 PDT
Custom Search