My ligand is an indolyl-quinolinium ring with a +2 charge. When I use
prepare the frcmod file for my ligand after the esp calculation in
gaussian, I get something as following in the frcmod file:
ca-ca-cc-cc 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
ca-ca-cc-cf 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
When I do the simulation, some unusual planarity changes occur in an
otherwise planar, aromatic ring. We speculate that it might be due to the
error in ligand preparation where the penalty scores are really high in the
frcmod file. So we are searching for methods to solve this problem. For the
same, we need to know about the forcefields for small molecule ligands.
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Received on Fri Apr 17 2020 - 06:30:02 PDT
