Dear Ibrahim,
maybe an installation of the newest AmberTools16 suite, where the
program sander is now included, could solve your problems. The
AmberTools are available for download from the Amber web site:
http://ambermd.org/#AmberTools
You could install them in addition, i.e. in a separate directoy
structure, to your existing Amber12 tree.
Regards,
Anselm
Am 10.11.2016 11:56, schrieb Ibrahim Said:
> Dear Amber users
> I am trying to study unfolding of a solvated protein applying SMD.
> Unfortunately,
> the box dimensions are too long (800x 100x 100 Ang.) and during
> minimization I got the following message nfft1-3 too large! check on
> MAXNFFT in ew_bspline.f.
> I found in the amber mailing list archive a message from Ross walker as
> follows "apply the attached bugfix to $AMBERHOME/src/sander/ew_setup.f and
> then, after recompiling, you should find that your simulation will now
> work".
> Unfortunately, I do not know how can I recompile Sander suite only. Any
> hand will be appreciated. My system is ubuntu12 and Amber program is 12.
>
> All the best,
>
> Ibrahim
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Received on Thu Nov 10 2016 - 03:30:02 PST
