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
http://research.bmh.manchester.ac.uk/bryce/amber.
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 04 2019 - 05:00:02 PST
