On Tue, Aug 28, 2018, Antonio Amber Carlesso wrote:
>
> I am trying to correctly prepare a protein with a ligand.
>
> > loadMol2 MKC.mol2
Above is the wrong syntax: it should be "31J = loadMol2 MKC.mol2"
(assuming that, confusingly, the information for unit 31J is actually in
the file names MKC.mol2).
>
> Loading Mol2 file: ./MKC.mol2
> Reading MOLECULE named 31J
If you type "list" after this, I'm guessing you will see that there is
no unit named 31J in the list of available units
> Creating new UNIT for residue: 31J sequence: 966
> Created a new atom named: C21 within residue: .R<31J 966>
Above is consistent with the problem noted above.
This is an all-to-easy mistake to make. Maybe Scott (our resident tleap
fixer) can think about making the syntax of loadMol2 more like that of
loadOff. Until then, try modifying your script.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 28 2018 - 15:00:02 PDT
