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.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Thu Feb 17 2005 - 17:53:00 PST
