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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- application/octet-stream attachment: ATP.prep
Received on Sun Oct 16 2016 - 13:30:02 PDT
