AMBER: Coodinates not being unique

From: Nitin Bhardwaj <>
Date: Mon, 11 Dec 2006 18:50:41 -0600

Dear Amber uses,
      I am again having a strange problem in my simulation. I have a
hydrogen bonded to a phosphate ion whose atomtype is 'ho' that overlaps with
another Oxygen carrying a negative charge. When I run my simulations in NAMD
after making prmtop and inpcrd files, right from the first step of
minimization. I get the error "Not all atoms have unique coordinates". When
I say check <my unit>, there is no error/warning of any kind. All the atoms
are fine. I have also checked the inpcrd file to see if there are
any identical set of coordinates but everything is fine.
Now, one possiblity is that this happens because the Hydrogen almost
overlaps with Oxygen, but then I should not get this error in the first step
of minimization itself.

Has anyone seen this problem before?

Thanks a lot in advance.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Dec 13 2006 - 05:21:50 PST
Custom Search