AMBER Archive (2005)

Subject: AMBER: problem with ptraj and randomizeions

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Thu Feb 17 2005 - 11:56:24 CST

Dear AMBER users,

I have a problem with the randomizeions command in ptraj. I would like
to randomize
all the ions of my system away from my solute. I use the script below :
ptraj $name.top <<!
trajin $name.pdb
trajout $name.rand.crd restart
randomizeions :Cl- around :1-436 by 5.0 overlap 3.5
randomizeions :K+ around :1-436 by 5.0 overlap 3.5
go
!

I have used this script many times before and everything was allright.
But today, running this script on a new system, the program ended
correctly,
but when I look to my structure, I have still an ion which stays at less
than 5 angstrom
from the solute.
I tried to increase the cutoff to 8 angstrom but once again, one ion is
at less than 5 angstrom
from the solute.

Has anyone ever seen this problem before ?
Thanks for your answers,
Fabien 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu