Re: [AMBER] Methylated adenine parameter

From: David A Case <>
Date: Tue, 15 Nov 2016 08:15:59 -0500

On Tue, Nov 15, 2016, Kshatresh Dutta Dubey wrote:
> I have to simulate a system that contains methylated adenine assigned as
> 6MA in pdb. I found that parameters for 6MA is already in amber but as
> modified RNA ( leaprc.modrna08). I am unable to find the corresponding
> parameter for modified DNA in amber list of units in default paramters.
> I will appreciate if someone can suggest me where can I find parameter for
> methylated adenine to be used for DNAs. I have very little experience of
> nucleic acid simulations.

Try this: edit the nucleic12.lib file, making a copy of DA, and call it 6MA
(or something else). Change the base so that it looks like the base in in the
6MA entry in all_modrna08.lib file -- you will mainly be editing atom types
and charges.

You can also visit the R.E.D. server to see if this has already been done, or
to undertake the project there.

...good luck...dac

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Received on Tue Nov 15 2016 - 05:30:03 PST
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