On Wed, Jun 20, 2007, backy wrote:
> Parameter file was not saved.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You had error in the leap step, never actually made a prmtop file.
>
> ATOM 1 C ACE A 1 70.110 65.868 39.946 1.00 0.00
> ATOM 2 CA ALA A 1 70.537 66.473 38.657 1.00 0.00
> ATOM 3 C ALA A 1 69.639 67.664 38.316 1.00 0.00
> ATOM 4 O ALA A 1 68.434 67.654 38.604 1.00 0.00
> ATOM 5 CB ALA A 1 70.456 65.436 37.551 1.00 0.00
> ATOM 6 N THR A 2 70.232 68.687 37.711 1.00 0.00
> ATOM 7 CA THR A 2 69.495 69.875 37.320 1.00 0.00
> ATOM 8 C THR A 2 69.540 70.004 35.797 1.00 0.00
You have to add an entire ACE residue (or at least the heavy atoms), not just
one C atom. Also, you have two residues labelled "1" (ACE and ALA), which
will confuse LEaP. Also, there is no N atom for the ALA.
Don't try to run sander until you get LEaP running the way it should.
...good luck...dac
p.s.: are you sure you want to add the capping groups to a complete protein?
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Received on Sun Jun 24 2007 - 06:07:09 PDT
