Re: [AMBER] Parameter file GTP or GMP containing tRNA

From: David A Case <>
Date: Mon, 4 Nov 2019 07:36:17 -0500

On Mon, Nov 04, 2019, student_cbc_1 nnlab wrote:
>We plan to run classical MD simulation of a tRNA molecule containing GTP or
>GMP as a base at 5' end before G1. How should we prepare the parameter file
>along with the frcmod and mol2 file for that type of tRNA to load in AMBER?

I've attached a terminal GMP unit; this is named "G5", so if you load
this after loading leaprc.RNA.OL3, this G5 will take the place of the
"regular" G5 unit that was in the RNA.OL3 file. I don't think you will
need any frcmod file for this.

You could do a similar thing from a 5' GTP residue, probably starting
from the GTP parameters at

Above assumes that you have a PDB file with coordinates for the GMP or
GTP leaders. That is, this does not solve the problem of getting
starting coordinates.

...hope this helps....dac

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Received on Mon Nov 04 2019 - 05:00:02 PST
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