RE: AMBER: Sander : Vrand flag

From: Furse, Kristina Elisabet <>
Date: Tue, 24 Aug 2004 13:47:38 -0500

> (Interestingly, with another system which has no manually added water
> molecules the simulation goes fine. Eventhough the temperatures and high,
> similar to above.)
Just a little note on this comment. It may be that in the process of
transforming your initial system into a pdb, manually adding more water and
reading back into leap, you lose your solvent cap information (the restraining
directions, not the waters themselves), and therefore see the water boil off.
I've never worked with caps, but the above is true for periodic boxes (in
amber7, anyway). Once you go to pdb (no box or cap info), then back into leap,
you need to reset the box info. Anyway, Ross' suggestion that you manually add
waters first, then set up the cap should take care of this as well if it is an

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Aug 24 2004 - 19:53:00 PDT
Custom Search