Re: [AMBER-Developers] TER card issue with ambpdb

From: Ilyas Yildirim <>
Date: Tue, 3 Jul 2012 16:03:46 -0500 (CDT)

> By the way, I can run both prmtop files with PMEMD and SANDER. Why do you say that pmemd should not work with this type of a system?
> pmemd has a check on intermolecular bonds, and an input variable that controls whether these are allowed or not.  The current source code sets no_intermolecular_bonds = 1.  Since your molecules are not
> contiguous, pmemd should detect that some atoms in molecule 1 are bonded to atoms in molecule 2 (simply because with discontinuous molecule residues there's no way a simple list of molecule sizes can
> give enough information to identify them).  Ergo, unless you explicitly set no_intermolecular_bonds=0 in the pmemd input file, my thought is that a fatal error should be produced.  (I've seen it happen
> before, so I'm not just spouting what I *think* the code should do)

Jason -

I did not set no_intermolecular_bonds to 0. In the output files, I see

| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1

I can send you the prmtop and inpcrd files (and the pmemd/sander input
script) if you would like to test it.


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Received on Tue Jul 03 2012 - 14:30:02 PDT
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