I'm having trouble adding ions.
Here is what I did
edited pdb.
loaded into xleap (leap added a missing atom and H's)
saveoff .lib
saveoff .pdb
saveamberparm pdb .prmtop .inpcrd
and I get:
WARNING: The unperturbed charge of the unit: -3.000000 is not zero.
(files were created)
therefore I tried adions pdb Na+ 0
(argument #1 is a type string unit)
am1=createUnit pdb
addions am1 Na+ 0
Na+ has a charge of 0.
addIons: Can't neutralize.
from what i understand I created a unit and tried to neutralize, but... no
bueno. The endgame is to do a simple minimization of this protein.
any suggestions on how to get un-stuck?
Thanks and sorry for the simplicity of the question. I did search the
archives and tutorials, but I'm a bit lost. I'm missing something simple.
Jonathan
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Received on Tue Sep 11 2012 - 11:00:11 PDT
