It looks like you need to make LIG 1 atom CD2 a connect[0/1] atom in
your residue template for LIG. I can't find any web pages for it, so
checking the manual would be in order.
Bill
On 10/16/16 1:09 PM, Paul Meister wrote:
> Hello,
>
> I'm trying to build my topology and coordinate files for my enzyme so I can
> begin my MD, but I get an error during LEaP which I'm not sure how to
> solve. I have loaded parameters for two different ligands, but I'm not
> entirely sure what this error is telling me.
>
> One sided connection. Residue: default_name missing connect1 atom.
> ERROR: Comparing atoms
> .R<ATP 390>.A<O3B 7>,
> .R<ATP 390>.A<O1G 9>,
> .R<ATP 390>.A<O2G 10>, and
> .R<ATP 390>.A<O3G 12>
> to atoms
> .R<ATP 390>.A<O3B 7>,
> .R<LIG 1>.A<CD2 1>,
> .R<ATP 390>.A<O1G 9>, and
> .R<ATP 390>.A<O2G 10>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named CD2 from LIG did not match !
>
> Everything before this was running fine. I have also done this same process
> before for another enzyme, but I haven't seen this error. Is there some
> kind of issue with the ATP parameters? I have uploaded the prep file and
> frcmod file for ATP.
>
> Thank you,
>
> Paul Meister
>
>
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Received on Sun Oct 16 2016 - 14:00:03 PDT
