On Tue, Nov 15, 2011, Crystal.CHIA-YU Ku wrote:
>
> In ions94.cmd, I modified first MG to Mg+ in "createAtom" after
Now you will be getting a residue named "Mg+" (use the "list" command
in tleap to see what units are loaded, and the "desc" command to find out
what each unit contains.)
But in your pdb file, you name the residue "MG". The two have to match, and
you can either edit the Amber library or edit the pdb file to get residue
names to match up. In your case, editing the ions94.cmd file probably led you
in the wrong direction. But it is good to learn how to understand LEaP
errors. Here is the message from your leap.log file:
Unknown residue: MG number: 80
This means that leap didn't know what to do with residue 80, named "MG".
Once you have a unit named MG (loaded into leap before the loadPdb command),
you should be good to go.
[Except, of course, for the problem with the thiamine monophosphate, subject
of a separate email.]
....dac
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Received on Tue Nov 15 2011 - 18:30:03 PST
