Dear Sir/Madam,
I would like to run NED in amber10. I found sander.PIMD was used in tutorial 5 for amber9. As no sander.PIMD can be found in my AMBERHOME/exe directory, I cannot run this job as in the tutorial.
AMBERHOME/exe/sander.PIMD -O -i md-ala-neb-smallk_1.in -o md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
so, I tried to submit the job as follows by using sander.MPI. However, it did not works. The file stop by complaining that "Flags: MPI ***This version will not accept topology files that were created by addles, with NPARM=1 use a version compiled with -DLES"
AMBERHOME/exe/sander.MPI -O -i md-ala-neb-smallk_1.in -o md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
>From the archive, some report the use of sander.LES.MPI, so I also give it a try. I submit the job in tutorial 5, section 4 as follows, but The output file stop at weight changes/NMR restraints.
AMBERHOME/exe/sander.MPI -O -i md-ala-neb-smallk_1.in -o md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
Could you mind to let me know how to run the NED in amber10?
Best regards,
Cat
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Received on Fri Aug 20 2010 - 03:00:05 PDT
