Re: [AMBER] parameter file for dUTP

From: Zachary Fallon <>
Date: Thu, 30 May 2019 13:55:20 -0400

Hi Arthur,

I don't believe there is a pre-made dUTP parameter file, but you can easily
put one together using Dr. Carlson's triphosphate parameters and dU
parameters from your favorite RNA force field. I have done this before with
dCTP and dTTP and I get good results (in DNA systems), so it should be
doable with dUTP as well. You will need to build a frcmod and lib file.

Hope that helps, best of luck!


On Thu, May 30, 2019 at 9:04 AM sunyeping <> wrote:

> Dear everyone,
> I would like to do MD similation with a protein in complex with dUTP
> (2'-Deoxyuridine-5'-triphosphate). Is there parameter file for dUTP ? Or
> should I prepare the parameter file for it? And how to prepare it?
> Best regards,
> Arthur
> _______________________________________________
> AMBER mailing list

Zachary Fallon, PhD Candidate
Dr. Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (914) 703-1010 <(914)+703+1010>  Email:  zachary.fallon.stonybrook.
AMBER mailing list
Received on Thu May 30 2019 - 11:00:02 PDT
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