Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA

From: David A Case <>
Date: Mon, 7 Sep 2020 08:31:56 -0400

On Mon, Sep 07, 2020, Jenny 148 wrote:
>I have a few systems of RNA- protein and DNA- protein complexes to work
>with. My RNA strands begin with a GTP and since I am a beginner, I do not
>know how to parametrize the GTP when it is in part of an RNA. Similarly, I
>need to know how to include the 5' terminal phosphates of the DNA as well.
>Could someone give some guidance regarding how to perform these tasks?

If you have mono-phosphates at the 5' terminal ends of either DNA or RNA,
then use loadOff to lead terminal_monophosphate.lib after loading the standard
leaprc files for DNA or RNA. (Your email wasn't clear about whether the DNA
5' phosphates were mono- or poly-phosphates).

If you have a 5' GTP residue, you should be able to use the attached
files. These were derived from the stand-alone GTP residues prepared by
Heather Carlson and co-workers (see the contributed parameters database),
but modified to act as a 5' residue for RNA. Name the 5' residue "GTP"
in you input pdb file-- this is what the PDB itself does, but not all
PDB-like files follow this standard.

...good luck....dac

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Received on Mon Sep 07 2020 - 06:00:04 PDT
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