On Mon, May 16, 2011 at 6:42 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Dear Amber users,
>
> Below is the error I encountered when running a batch file of sander for MD
> runs following 2-step minimization:
>
> */var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 17: 14885
> Segmentation fault /usr/local/amber10/exe/sander -O -i ./file-in/
> wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
> ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x ./results/ndm_md1.mdcrd
> -ref ./results/ndm_min2.rst
>
> Unit 30 Error on OPEN:
> ./results/ndm_md1.rst
> /var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 25:
> ./results/ndm_md2.rst: No such file or directory
> *
>
I don't think you copied everything over correctly. Here it says that
./results/ndm_md2.rst doesn't exist, but I don't see anywhere above where
you used that file.
> could anyone please give me a hint about this? I just dont understand why
> it
> happened 'cause it ran fine for other molecules before. And why didnt it
> occur during minimization?
>
> Thank you very much, and really looking forward to your reply.
>
> Regards,
> Chinsu
>
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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 Mon May 16 2011 - 04:30:04 PDT
