In addition to Hannes’ very helpful advice, I would strongly recommend upgrading to AmberTools 14. Amber hasn’t used an “exe” directory to hold its programs since Amber 9 or 10 (I can’t remember which). In any case, *many* bugs have been fixed since then, and if you encounter any problems we will almost certainly tell you to upgrade before helping with the problem (since there is a good chance it will have been fixed in the meantime).
Hope this helps,
Jason
> On Dec 9, 2014, at 2:28 AM, hannes.loeffler.stfc.ac.uk wrote:
>
> Not easy to spot the error in this data pile. Better attach each file separately and only paste the principal inputs to leap and the error message to the body of the mail.
>
> I think what you want to do is more like
>
> source leaprc.gaff
> SAL = loadmol2 sal1_h.mol2
> mods = loadamberparams sal1_h.frcmod
> saveoff {SAL mods} sal1_h.lib
>
> and then
>
> source leaprc.gaff
> loadoff sal1_h.lib
> comp1 = loadpdb comp1.pdb
>
>
> Your use of saveoff shouldn't even work. Use the list and desc commands to see what actual names you are using and storing.
>
> Cheers,
> Hannes.
>
>
> --
> Scanned by iCritical.
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 09 2014 - 04:30:03 PST
