[AMBER] atom type for N bond to conjugated chain using antechamber

From: zhonghe xu <zhonghexu01.163.com>
Date: Fri, 5 Jul 2013 11:32:11 +0800 (CST)

 Hi all:
I prepare biguanide ligand for MD using antechamber with a command "antechamber -i xx.pdb -fi pdb -o xx.mol2 -fo mol2 -c bcc".
I have a question about atom type for N(highlighted in red) on conjugated chain, which were assigned to nh(N connected to aromatic ring in gaff). However, there is no aromatic ring(even a ring ) in molecular structure or file generated by antechamber.I wonder whether it is needed to modification or correction for this atomtype ? Thank in advance !
Best regard

  R2 N N
   | || |
 R1-- N --C--N==C--N

zhonghe xu

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Received on Thu Jul 04 2013 - 21:00:14 PDT
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