Re: [AMBER] MPI error

From: Robert Duke <>
Date: Wed, 29 Jul 2009 13:05:57 +0100

This sounds like a bad prmtop, or at least that is what the code that
produces this message is intended to catch. Is this amber 9 you are
running? I would have to actually look at your mdin and prmtop (plus inpcrd
to be able to test) to have a clue whether the molecule data is truly bad,
or if there is a potential bug. Typically, this sort of mess occurs, I
believe, when there is a problem of some sort with special residues and
bonding patterns in the pdb used to create the prmtop/inpcrd. In amber 10,
the problem sort of goes away, or perhaps it would be better to say that the
division granularity is finer, so you may or may not have a problem running
on amber 10. Anyway, you may want to send your input files directly to me
(including pdb if possible) so I can figure out what is strange about the
setup, or if there actually is a pmemd bug (unlikely for this, but one
should not make assumptions).
Regards - Bob Duke

----- Original Message -----
From: "vhakkim boy" <>
To: <>
Sent: Wednesday, July 29, 2009 5:44 AM
Subject: [AMBER] MPI error

> dear amber users
> I'm having a strange problem running an MPI simulation with
> pmemd. When I try to start the calculation it fails with
> Bad residue/molecule data in prmtop!
> |Residue 260(atoms 4074- 4076) is in multiple molecules.
> can any one tell me what is the solution to this proplem
> _______________________________________________
> AMBER mailing list

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Received on Wed Aug 19 2009 - 19:40:13 PDT
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