RE: AMBER: Bad residue/molecule data in prmtop

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 25 Jul 2007 07:17:00 -0700

Dear Neva,

Can you try building the prmtop file again from scratch and see what you
get. Then please post a copy of exactly what you did to create this prmtop
file including the original pdb you used and the commands you gave Leap etc.

Do you get the exact same problem if you run in serial?

All the best
Ross

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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of neva.mmb.pcb.ub.es
> Sent: Wednesday, July 25, 2007 06:03
> To: amber.scripps.edu
> Subject: AMBER: Bad residue/molecule data in prmtop
>
> 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
>
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Received on Sun Jul 29 2007 - 06:07:11 PDT
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