Hi Carlos,
Thank you very much for the prompt answer.
The periodic box of size 120 x 120 x 120 A that I built contains SOD1 and
20 Na+ counterions; I used tleap to build the parm7 and inpcrd files.
The Amber 2024 Reference Manual does not recommend using ISEXI for a
protein, whereas the ALPB approximation looks very appropriate.
May I ask you to please help me out in preparing the corresponding input
file portion for ALPB?
Best regards,
Andriy
On Tue, Jul 30, 2024 at 10:41 AM Carlos Simmerling <
carlos.simmerling.stonybrook.edu> wrote:
> I do see that Onufriev's model is discussed in the Amber 24 manual section
> 4.2, you should look at that if you have not already.
>
> On Tue, Jul 30, 2024 at 12:38 PM Carlos Simmerling <
> carlos.simmerling.stonybrook.edu> wrote:
>
>> I don't think Amber currently supports the combination of periodic box
>> and implicit solvent, but I'm surprised you don't get an error message
>> about it. Also, implicit solvent with explicit ions is a fairly new
>> development, see recent work by the Onufriev group for info. I think that
>> tleap may allow you to build this, but the resulting default parameters are
>> not likely to be very well optimized right now.
>>
>>
>> On Tue, Jul 30, 2024 at 12:30 PM Andriy Kovalenko via AMBER <
>> amber.ambermd.org> wrote:
>>
>>> Hello,
>>>
>>> I am trying to run PMEMD minimization, heating, equilibration, and
>>> production stages for the SOD1 biomolecule with Na+ counterions in
>>> ambient
>>> water in a periodic box.
>>> However, Cedar terminates the run with an error message:
>>> - Program received signal SIGSEGV: Segmentation fault - invalid memory
>>> reference.
>>> Attached please see the output files and the input files (except for
>>> 3cqp_3_amb_period.parm7 which is of size 3,673K) for the heating run.
>>>
>>> My previous runs of this set but without a periodic box succeeded.
>>>
>>> Please advise how to resolve this issue with the periodic box runs.
>>>
>>> Sincerely,
>>>
>>>
>>> Dr. Andriy Kovalenko
>>>
>>> Researcher
>>> Department of Biological Sciences
>>> University of Alberta
>>> CW 405, Biological Sciences Bldg.
>>> Edmonton, Alberta, Canada T6G 2E9
>>>
>>> Tel: 780-940-7477 (cell)
>>> e-mail: andriy.kovalenko.ualberta.ca
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Tue Jul 30 2024 - 11:30:02 PDT
