Good morning!
[Developers: Amber does a piss-poor job of supporting modified
nucleotides.
The all_modrna09 files are not compatible with current RNA atom types, and
there are only scattered instances of modified deoxy-nucleotides. We should
also have standard entries for the 2'-O-methyl modifications. I'm hoping
that some DNA/RNA person will step up to help get this organized. Might
this be a good summer undergrad project?]
Funny you should mention this, Dave -
After spending more time than I wanted to spend putting together DU LEaP
library files, I have a SURF (paid fellowship) project this summer that
will cover some of what you mentioned below.
My main interest is in chemical modifications to RNA that are being used in
siRNA drugs, so the 2'OMe and 2'F, etc. parameters, which I planned on
incorporating into at least one RNA force field, but I can follow up with
other modifications too.
If anyone else is moving forward with this, I'd be happy to
help/collaborate, and potentially can host a Summer student (virtually, of
course).
-Christina
---------- Forwarded message ---------
From: David A Case <david.case.rutgers.edu>
Date: Wed, Jan 20, 2021 at 8:31 AM
Subject: Re: [AMBER] Creating input files using tleap
To: AMBER Mailing List <amber.ambermd.org>
On Tue, Jan 19, 2021, Nicy yadav wrote:
>
>I am a beginner in using AMBER. I have been trying to create some input
>files for a DNA sequence that contains 5-methyl-cytosine. I have an input
>PDB file that contains DNA complexed with an enzyme, however I am just
>interested in the conformation of the DNA molecule. Can you please check if
>I am following the right steps?
>
>1. Delete everything from the PDB that is not related to the DNA
>sequence.
This is correct. To get started, I'd suggest that you also remove the
methyl group from the 5CM, and re-name the residue " C". This will
allow you to become familiar with doing a simulation on a standard piece of
DNA; you can return to the 5CM problem later.
>
>2. pdb4amber -i orig.pdb -o new.pdb --reduce –dry
Generally recommended, but not really needed for your case.
>
>3. How do we choose the force field? parmbsc1 or OL15? Can we use
>both?
You can use one or the other, but not both. Further, these force fields
come built-in with Amber, so you don't need to go trying to find files on
the web, since the latter might be out of date, or not exactly the right
format. Do this in tleap:
source leaprc.DNA.OL15 *or*
source leaprc.DNA.bsc1
Both parameterizations are quite good: see the discussion in Section 3.2 of
the Reference Manual for more information.
>
>5. archive.ambermd.org/201910/0005.html
I've not used this file myself, but it should be useful, especially with
bsc1. Others in the field may be able to say more here.
[Developers: Amber does a piss-poor job of supporting modified nucleotides.
The all_modrna09 files are not compatible with current RNA atom types, and
there are only scattered instances of modified deoxy-nucleotides. We should
also have standard entries for the 2'-O-methyl modifications. I'm hoping
that some DNA/RNA person will step up to help get this organized. Might
this be a good summer undergrad project?]
>loadAmberPrep dmc.in
>loadOff parmMC.lib
Above is correct. But I'd still think that a beginner should spend a few
days with a standard system. Be sure to checkout out tutorial 5.2, if you
have not already done that.
...good luck....dac
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Wed Jan 20 2021 - 06:30:04 PST
