AMBER: problem with Thermodynamic Integration

From: Martin Stennett <>
Date: Wed, 19 Sep 2007 12:46:30 +0100

I'm trying to run thermodynamic integration, and have followed the manual pretty much to the letter so far.
The only problem I've run into is that when I try to run

prun -n 2 sander -ng 2 -groupfile

I get the error message:

>mdfil: Error unknown flag: -ng
>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

It strikes me as odd that the flag is unknown, but also in the list of known flags... should they be in a specific order??

  Martin Klefas-Stennett

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Sep 23 2007 - 06:07:07 PDT
Custom Search