> 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.
Ilyas,
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Received on Tue Jul 03 2012 - 14:30:02 PDT
