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 <
zachary.fallon.stonybrook.edu>
Sent At:2019 May 31 (Fri.) 01:55
To:孙业平 <
sunyeping.aliyun.com>; AMBER Mailing List <
amber.ambermd.org>
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!
--Zachary
On Thu, May 30, 2019 at 9:04 AM sunyeping <sunyeping.aliyun.com> 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
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>
--
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.
<zachary.fallon.stonybrook.edu>edu
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Received on Thu May 30 2019 - 15:00:03 PDT
