Hello Zachary,
Thank you for your reply.
I downloaded a "frcmod.phos" file from Dr. Richard Bryce's Amber Parameter Database (The download link is
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos). I guess it is the triphosphate parameter file, isn't it?
I have browsed amber/dat/leap directory, and opened many lib and frcmod files but still don't know which one contains the dU paramters. Could you tell me which one I can try to use?
Best regards,
Arthur
------------------------------------------------------------------
From:Zachary Fallon <
zachary.fallon.stonybrook.edu>
Sent At:2019 May 31 (Fri.) 06:12
To:孙业平 <sunyeping.aliyun.com>; AMBER Mailing List <
amber.ambermd.org>
Subject:Re: [AMBER] parameter file for dUTP
Hey Arthur,
Welcome to Amber! Your first question is a little tricky because there are
many, many RNA force fields. I am not an RNA person so I am not familiar
with which (if any) are considered 'standard', so I suggest you consult the
literature for reviews and maybe look for how other people have simulated a
system similar to yours. Otherwise, the force field files are located in
amber/dat/leap; you'll find the leaprc, lib, and frcmod files for the
various parameter sets in the different sub-directories from there.
As for Dr. Carlson's triphosphate parameters, I believe you can find those
on Dr. Richard Bryce's Amber Parameter Database. Those parameters are for
GTP and ATP though, so you'll likely have to trim off the sugar + base part
of them and insert the dU parameters from another RNA force field. Here is
the paper where Dr. Carlson published her phosphate parameters:
https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.10262
Best of luck!
--Zachary
On Thu, May 30, 2019 at 5:38 PM sunyeping <sunyeping.aliyun.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> 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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>
--
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 Tue Jun 04 2019 - 13:00:03 PDT
