AMBER: Bad residue/molecule data in prmtop

From: <>
Date: Wed, 25 Jul 2007 15:03:19 +0200

Hi all,

I have a problem with a prmtop file,I think. When I run a MD of my system
(double strand DNA with a complex) with amber 8, parallel run, I have the
following message:

| ERROR: Bad residue/molecule data in prmtop!
| Residue 13(atoms 374- 404) is in multiple molecules.

Then I generate a pdb from prmtop and coordinate file with ambpdb,
but it give me a pdb file with a TER in the middle of the 13 residue, instead
after the 12 residue.
I carefully double-checked that the sequence and names of atom types correspond
to the standard library. Moreover the complex binding the DNA is placed after
the DNA.
What I can do? Which is the problem? Can you help me
Thank you a lot


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Received on Sun Jul 29 2007 - 06:07:09 PDT
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