Re: [AMBER] Error: Sander output is missing values

From: Jason Swails <>
Date: Tue, 20 Apr 2010 11:41:03 -0400


On Tue, Apr 20, 2010 at 11:08 AM, Hyma vathi <>wrote:

> Thank you for the reply. But I am unable to find where the error is. The
> solvated prmtop is consistent with the trajectory i have given in -y flag.
> But for the mdcrds the created the structures were distorted. The
> masks are matching in the namelist. Please let me know how can I spot the
> error I tried to attach the prmtop files but failed.

You should not have to specify the masks anymore. As long as the ligand
residues appear as a continuous sequence in the complex topology file, will correctly guess the appropriate masks for the ligand and
receptor. It will also print out the guessed mask in the final output file
so you can check it. Note that this is a good error check. If
fails to correctly guess the mask, it is likely that your topology files are

Note, too, that it's not just important for the solvated_prmtop to be
consistent with the mdcrd passed to It is also important that
the complex_prmtop, receptor_prmtop, and ligand_prmtop be consistent with
_MMPBSA_complex.mdcrd, _MMPBSA_receptor.mdcrd, and _MMPBSA_ligand.mdcrd,
respectively. If these structures look warped and/or distorted, then your
prmtops are inconsistent. Here are a couple things to look out for:

Any waters and/or ions present in your solvated_prmtop are stripped, and so
should not be present in any other topology file (complex, receptor, or
ligand). The number of atoms in the complex prmtop must equal the sum of
the number of atoms in the receptor_prmtop plus the number of atoms in the
ligand_prmtop. (This will be checked for automatically in a future release

Good luck!

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Tue Apr 20 2010 - 09:00:04 PDT
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