Hello,
The version on the web has been updated recently, so if you have not
downloaded this new version within the past couple days, you should
download this new version (and re-run the installation process). The
new version of the script does not require ligand_mask and
receptor_mask as inputs anymore. It will successfully guess the
ligand and receptor masks as long as the ligand residues are
continuous within the complex topology file (as it is in your system).
Please try this new version. As a side note, this is failing because
commas are not permissible characters in input variables.
Good luck!
Jason
On Thu, Feb 18, 2010 at 4:26 PM, Workalemhu Berhanu
<wberhanu.mail.ucf.edu> wrote:
> Dear amber users
>
> I am trying to calculate the binding energy between a peptides receptor and a peptide ligand.
> My receptor is the residues 1-37 and 75-111 and my ligand is a residue 38-74
> I tried a receptor mask =:1-74, 112-185 and ligand mask=:75-111.
> I got the error message
> Warning: Input error! "112-185 ligand_mask=:75-111" is an invalid option.
> 5-mer_md1.mdcrd: Permission denied.
> Would you please help me in finding what is wrong on my receptor mask and ligand mask? I am using the new Python Version and its is installed and tests performed as in the tutorial 3
>
> Thank you
> Workalemahu
>
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Feb 18 2010 - 14:00:05 PST
