Thanks a lot David. Your suggestions are very helpful.
On Wed, 20 Jan 2021, 1:31 pm David A Case, <david.case.rutgers.edu> wrote:
> 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 the web, since the latter might be out of date, or not exactly the right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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Received on Wed Jan 20 2021 - 06:30:06 PST
