Re: amber-developers: What happened to sander's '-y' option?

From: Gustavo Seabra <>
Date: Thu, 01 Mar 2007 18:40:56 -0500

David A. Case wrote:
> On Thu, Mar 01, 2007, 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
> Please see (look at second line)
> I know Carlos has talked about getting this working correctly for Amber 10,
> but I believe that has not yet been done.
> ....dac
Thanks Dave. But I must be missing something here... even with '-x' it
doesn't quite work. If I try:
sander -O -x reaction.crd -p

I get one of those ugly errors that it can't open unit 9 (the inpcrd
file). If I then include an inpcrd file, like:
sander -O -c inpcrd -x reaction.crd -p

sander now dies with the message:
 Error in trajectory file
 error in trajene()

But the trajectory in reaction.crd is ok (I tried openeing in vmd). So
it seems to me that just using '-x' instead of '-y' as suggested in the
erratum is not enough, or I am really missing something here...

Received on Sun Mar 04 2007 - 06:07:46 PST
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