AMBER Archive (2007)

Subject: AMBER: Bad residue/molecule data in prmtop

From: neva_at_mmb.pcb.ub.es
Date: Wed Jul 25 2007 - 08:03:19 CDT


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
please
Thank you a lot

Neva

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu