Re: AMBER: pmemd9 issue

From: Robert Duke <>
Date: Sun, 2 Jul 2006 07:12:11 -0400

Brent -
I cannot assert this with absolute certainty, but my first guess would be that the prmtop is incorrect; it turns out that it is (or at least has been in the past) rather easy to build a system with incorrectly defined molecules over the atoms, I believe depending on what the input to xleap or tleap looks like. I encountered these problems in the past with inputs, and it only causes execution problems in parallel runs, a function of how the load is assigned. You might want to send the prmtop, inpcrd, and mdin to me, if you don't mind, and I will do further analysis. I am still working on my first cup of coffee here, but will fire up my source machines and take a look at the code to refresh my memory as to exactly what triggers this problem and what the ramifications are.
Regards - Bob Duke
  ----- Original Message -----
  From: Brent Krueger
  Sent: Saturday, July 01, 2006 11:45 PM
  Subject: AMBER: pmemd9 issue

  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.



  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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Received on Wed Jul 05 2006 - 06:07:07 PDT
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