On Mon, 16 May 2011, Chinh Su Tran To 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:
your input coordinate file "ndm_md1.rst" is not in the directory where you
run sander. either copy "ndm_md1.rst" to the sander working directory
or give the full path of "ndm_md1.rst" file in command line.
Santosh.
> ./results/ndm_md1.rst
> /var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 25:
> ./results/ndm_md2.rst: No such file or directory
> *
> 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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Received on Mon May 16 2011 - 01:00:03 PDT
