Hi,
Yes that looks like the frcmod file for the di- and triphosphates, but keep
in mind you'll need a lib file as well.
I am unfamiliar with RNA force fields, so I can't say if there are any
existing parameters for dU. If there are not, you will have to make them
yourself as Dr. Case described above: merging the lib and frcmod files of
dT's base and sugar with those of the triphosphate's, then removing the
methyl.
Regards,
Zachary
On Tue, Jun 4, 2019 at 3:52 PM sunyeping <sunyeping.aliyun.com> wrote:
> 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
> > > _______________________________________________
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> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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> 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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Received on Tue Jun 04 2019 - 16:00:01 PDT
