AMBER Archive (2006)

Subject: AMBER: pmemd9 issue

From: Brent Krueger (kruegerb_at_hope.edu)
Date: Sat Jul 01 2006 - 22:45:11 CDT

Hey there AMBER gurus!

I'm having a strange problem running an MPI simulation with pmemd.
When I try to start the calculation it fails with:

| ERROR: Bad residue/molecule data in prmtop!
| Residue 131(atoms 1990- 2026) is in multiple
molecules.

But I can successfully run the calculation using a serial version of
pmemd, with a serial version of sander, and with a parallel version
of sander, so I think the prmtop and rst files must be fine. (I can
also read the prmtop file with ptraj or rdparm or VMD without an issue.)

This is all amber9 built with gcc version 4.0.2 20051125 and ifort
version 9.0 and lam 7.1.2. The hardware is opterons with gigE.

I have run the test suite and everything passes nicely. Any ideas?
The prmtop and rst files are a bit large so I hesitate to email them
over the whole list, but if someone is interested I'd be happy to
send them on.

Cheers,
Brent

__________________________________________________________________
Brent P. Krueger phone: 616 395 7629
Assistant Professor fax: 616 395 7118
Hope College SC 2120
Department of Chemistry
Holland, MI 49423

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