AMBER Archive (2009)

Subject: Re: [AMBER] MPI error

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jul 29 2009 - 07:05:57 CDT


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" <vhakkim_at_gmail.com>
To: <amber_at_ambermd.org>
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
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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