I'm confused as to what your receptor and ligand residues are exactly, but
you should be able to use something like this if I'm reading your residue
numbers correctly (i.e. if your receptor residues are 1-37 and 75-11, and
your ligand residues are 75-111).
receptor_mask=:1-37:75-111, ligand_mask=:38-74
Good luck!
-Bill
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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Received on Thu Feb 18 2010 - 14:00:04 PST
