Re: [AMBER] Amber parameters for CPD and 6-4PP

From: Elvis Martis <>
Date: Tue, 9 May 2017 11:21:58 +0000

You can try AM1-BCC charges using antechamber.
For more details you can refer to this paper 10.1021/acs.biochem.6b00361 and maybe you can request the authors to give the parameters they have used.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: p.kartheek []
Sent: Tuesday, May 09, 2017 3:20 PM
Subject: [AMBER] Amber parameters for CPD and 6-4PP

Dear Amber users,
I would like to perform few preliminary MD simulations on cylobutane pyramidine dimer (CPD) and 6-4PP-DNA systems. Considering the time and resource constraints in parameterizing CPD, I want to use AMBER generated force filed parameters from some trustable sources. It would be of great help if anyone can help me with CPD parameters.
​Thanks in advance ​
P. Kartheek,
PhD Candidate, Computational Biophysical Chemistry, Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Marimuthu Krishan Group, 9701577399,, _______________________________________________
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Received on Tue May 09 2017 - 04:30:02 PDT
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