Dear Bill
Thank you
Now the mask problem seems to be solved and I am getting another error message after the calculation started as shown below.
-j: Command not found.
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi)
Error: Sander error! GB mdout file was not created.
I used the get the gas phase prmtop and inpcrd the example in the old version
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
com = loadpdb ras-raf.pdb
ras = loadpdb ras.pdb
raf = loadpdb raf.pdb
saveamberparm com ras-raf.prmtop ras-raf.inpcrd
saveamberparm ras ras.prmtop ras.inpcrd
saveamberparm raf raf.prmtop raf.inpcrd
Thank you
Workalemahu
>>> Billy Miller III <brmilleriii.gmail.com> 02/18/10 4:33 PM >>>
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 - 16:00:02 PST
