Re: [AMBER] Error: Sander output is missing values! VDWAALS = *************

From: Jason Swails <>
Date: Tue, 7 Dec 2010 14:15:40 -0500


Bill's email is completely correct, I just wanted to point out a potential
flaw in something you may be assuming. See below:

On Mon, Dec 6, 2010 at 11:21 PM, kamlesh sahu <>wrote:

> Hello amber users,
> I am running on trajectories obtained from MD simulation on a
> complex which contained four ZN ions and two Cl- ions. I did not remove Cl-
> before simulations. Can that be the reason why I am getting this error ? -
> Starting pb calculation...
> calculating ligand contribution...
> calculating receptor contribution...
> calculating complex contribution...
> Calculations complete. Writing output file(s)...
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -19824.2815 EPB =
> -4539.5565
> NOTE: All files have been retained for debugging purposes. Type
> --clean to erase these files.
> The output file has correct guess for ligand and receptor so I guess the
> prmtop and trajectories are compatible. Could you please tell me how to

The fact that the guess for the ligand and receptor are correct ONLY means
that the ligand, receptor, and complex topology files are consistent with
one another. That says nothing at all about whether or not they're
compatible with your trajectories. I would bet that if you visualize your
_MMPBSA_receptor.mdcrd file with your receptor prmtop (and the same with
your complex and ligand prmtops), you'll see that they're not actually

remove these Cl- ions from the trajectories before running (if Cl-
> ions are the problem). I just did pb calculations (not gb because it was
> saying 'bad atom type ZN')

You should probably remove ions unless they're explicitly part of binding,
since implicit solvent accounts for the salt effects via a debye screening
parameter (set via the variable "saltcon" in the input file). GB
is not meant to deal with explicit ions.

Also keep in mind that if you left the Cl- ions in your prmtop and wish to
strip them, then you'll have to create new prmtop files to be consistent
with the created trajectories.

Good luck!

> Thank you
> kamlesh
> --
> Kamlesh Kumar Sahu (post doc researcher)
> Riken, wako, Saitama, JAPAN
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Dec 07 2010 - 11:30:02 PST
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