[AMBER] Problem in setting parameters for the modified nucleotide

From: Xiaoting Mao <cos_mopolitan.163.com>
Date: Mon, 8 Apr 2019 21:10:58 +0800 (CST)

Dear all,

I have a non standard residue where guanine has been modified to N1-methylguanine. I combine ESP of two molecules(DMP and modified nucleoside) to calculate the point charges of the modified nucleotide.The next step is to create the lib file for the modified nucleotide. According to "http://archive.ambermd.org/201002/0013.html", firstly, I use antechamber to get atom types and force field parameters from the modified nucleoside. Then I use xleap,copy the standard guanine nucleotide(Guanine.pdb) to a unit, edit this new unit and create the needed modifications for N1-methylation. The atom types and charges must be added one by one, so sometimes I make mistakes. Save the results as an off file. Does it have another simple way to create this files(.lib file)?

Thank you in advance,
Xiaoting Mao
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Received on Mon Apr 08 2019 - 06:30:02 PDT
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