Re: [AMBER] parameter file for dUTP

From: sunyeping <>
Date: Fri, 31 May 2019 05:38:11 +0800

Hello Zachary,

Thank you for the help. Actually I am very new to amber. Could you tell me what is the RNA force field file containding du and where can I find it? Also where can I get Dr. Carlson's triphosphate parameters?

Best regards

From:Zachary Fallon <>
Sent At:2019 May 31 (Fri.) 01:55
To:孙业平 <>; AMBER Mailing List <>
Subject:Re: [AMBER] parameter file for dUTP

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.
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Received on Thu May 30 2019 - 15:00:03 PDT
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