Hi Case,
> 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.
Could you let me know how I can load a unit name MG? I have no idea to
do that...
> 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
I have questions about here above. In the original ions94.cmd, the
script for MG ion looks like this: i = createAtom MG MG 2.0.
According to your word above, the first "MG" is correct, and
supposely xleap should recognize MG in my receptor-ligand file. My
modified version Mg+ is wrong because it leads xleap not to recognize
MG. However, when I use the original in the early beginning, xleap
cannot use MG to recognize MG in my receptor-ligand file. Even if now
I already changed Mg+ to MG back, xleap still could not work. I really
do not understand why xleap cannot know MG in my file, even if in
ions94.cmd, "MG" is correct.
Sincerely,
Crystal
On Tue, Nov 15, 2011 at 6:06 PM, case <case.biomaps.rutgers.edu> wrote:
>
> On Tue, Nov 15, 2011, Crystal.CHIA-YU Ku wrote:
> > In ions94.cmd, I modified first MG to Mg+ in "createAtom" after
> 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 Wed Nov 16 2011 - 11:30:04 PST
