AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon May 01 2006 - 08:35:56 CDT

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

z3020110_at_student.unsw.edu.au 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
>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?
>
>Cheers,
>
>Francis Peters
>University of NSW
>Sydney, Australia
>
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