Have you tested on Amber 12?
On Tue, Jul 3, 2012 at 5:03 PM, Ilyas Yildirim
<i-yildirim.northwestern.edu>wrote:
> 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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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jul 03 2012 - 14:30:02 PDT
