[AMBER] atom type in a substituted pyrimidine

From: Sofia Vasilakaki <svasilak.chem.uoa.gr>
Date: Wed, 10 Jun 2020 10:10:50 +0300


what is the correct atom type of the carbon atoms in a substituted ring of
pyrimidine ?

I am trying to create the prmtop files for a small molecule which contain
a similar to thymine ring (with one CO though) and the atom type of the
carbon atoms of the ring are not aromatic, so during simulation the ring
does not remain planar. Should I source the dna leaprc in tleap?

Thank you,

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Received on Wed Jun 10 2020 - 00:30:04 PDT
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