Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py

From: Andrzej Dorobisz via AMBER <amber.ambermd.org>
Date: Thu, 8 Dec 2022 14:50:59 +0100

Hi,
I just uploaded the input data (22 GB) so you can download and test
cpptraj on it.

- file E81A.nc
https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/E81A.nc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134155Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=d01eba1bf5f637ccd55f1f28cdd0623ded099ad95a226a66108f8bc8cc1eeca9
<https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/E81A.nc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134155Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=d01eba1bf5f637ccd55f1f28cdd0623ded099ad95a226a66108f8bc8cc1eeca9>

- all other files (E81A.top + input-cpptraj.txt)
https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/cpptraj-SIGSEGV-files.zip?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134129Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=ca2814b488dbe69ed12261ad8b64b057870d155779cba7b147ce9d05af2f7f70
<https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/cpptraj-SIGSEGV-files.zip?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134129Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=ca2814b488dbe69ed12261ad8b64b057870d155779cba7b147ce9d05af2f7f70>

The error occurs after about 1 hour and 30 minutes.


Regards,
Andrzej


On 6.12.2022 16:43, Daniel Roe via AMBER wrote:
> Hi,
>
> On Tue, Dec 6, 2022 at 10:21 AM Andrzej Dorobisz
> <andrzej.dorobisz.cyfronet.krakow.pl> wrote:
>> Thank you for the quick reply. I can send the topology file but I don't
>> know how to extract frames from the trajectory file (../input/E81A.nc).
> The input would be something like:
>
> parm E81A.top
> trajin E81A.nc 1 10
> trajout E81A.1-10.nc
>
> -Dan
>
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Received on Thu Dec 08 2022 - 06:00:02 PST
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