Dear Santosh,
Thanks for your reply, but the path directing to ndm_md1.rst was defined
(i.e ./results/... as in my batch file). The key is the "ndm_md1.rst" had
not been created.
Regards,
Chinsu
On Mon, May 16, 2011 at 3:26 PM, Santosh Mogurampelly <
santosh.physics.iisc.ernet.in> wrote:
>
>
> 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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> >
>
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Received on Mon May 16 2011 - 04:30:03 PDT
