Dear Jason,
This is my batch file:
*/usr/local/amber10/exe/sander -O -i ./file-in/wat-min1.in -o
./results/ndm_min1.out -p ./results/ndm-wat.prmtop -c
./results/ndm-wat.inpcrd -r ./results/ndm_min1.rst -ref
./results/ndm-wat.inpcrd
/usr/local/amber10/exe/sander -O -i ./file-in/wat-min2.in -o
./results/ndm_min2.out -p ./results/ndm-wat.prmtop -c ./results/ndm_min1.rst
-r ./results/ndm_min2.rst
/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
/usr/local/amber10/exe/sander -O -i ./file-in/wat-md2.in -o
./results/ndm_md2.out -p ./results/ndm-wat.prmtop -c ./results/ndm_md1.rst
-r ./results/ndm_md2.rst -x ./results/ndm_md2.mdcrd
/usr/local/amber10/exe/ambpdb -p ./results/ndm-wat.prmtop <
./results/ndm_md2.rst > ./results/ndm_md2.pdb*
And the part below is the error I got:
**/var/spool/torque/mom_priv/*
*jobs/5731.bircibm.SC <
http://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<http://5731.bircibm.sc/>:
line 25:
> ./results/ndm_md2.rst: No such file or directory
*I double-checked and found that the ndm_md1.rst was not created, causing
the next command was not performed, so the second error led to "could not
open the ndm_md2.rst"
I viewed other threads from Amber archive titled "segmentation fault" saying
about "molecular size", but i dont think this error was addressed because i
ran the similar batch file for other larger molecules and they ran fine.
Is it possible that it was related to the TIP3PBOX of solvent I used? I used
TIP3PBOX 12 for this molecule.
Thanks for your reply, and hope more help.
Chinsu
On Mon, May 16, 2011 at 7:27 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 16 2011 - 05:00:02 PDT
