> Have you tested on Amber 12?
All the simulations were done using AMBER11, but I just tested on AMBER12. The
simulation runs without giving any error message. The input file is
Equilibration of the whole system: Temperature (20 ps)
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, cut = 8.0, ntr = 0, pres0 = 1.0, ntp = 1, taup = 2.0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, ig=6,
nstlim = 100, dt = 0.001,
ntpr = 1, ntwx = 1000, ntwr = 1000,
/
(Bad) prmtop was used in this test.
Ilyas,
>
> 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,
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Tue Jul 03 2012 - 14:30:03 PDT
