On Wed, Jul 21, 2010, Catein Catherine wrote:
>
> I am very interested to use NEB to calculate the conformation changes of
> a protein. I am using AMER10. According to the tutorial 5, I need to
> use sander.PIMD.MPI. However, I did not find this file in my working
> $AMBERHOME/bin directory. Could you mind to let me know if I need to
> request or install additional module on AMBER10 before I can use it?
> How about the addles, do I need to install addition module to use it on
> AMBER10? Thanks a lot.
The "older NEB tutorial" does seem to be outdated. You should know that
(a) NEB is (often) and *very* difficult procedure to get to work well;
(b) the implementation in Amber11 is much better than that in Amber10;
(c) the updated tutorial should be posted soon (Christina??). I'd strongly
recommend updating to Amber11 to run NEB.
[If you want to try the older code, see if sander.MPI will work; you should
already have an "addles" executable(?)]
....dac
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Received on Wed Jul 21 2010 - 05:30:03 PDT
