[AMBER] Sander code doesn’t output trajectory files

From: K Jan <10dunajkr.gmail.com>
Date: Wed, 6 Jan 2021 12:58:23 +0000

Dear all amber users

I have been simulating a molecule on Amber and I was wondering whether I
could ask you a question as I am unsure of how to visualize my molecule
with the output files that I have received from my sander code.

I`ve completed analysis on the molecule by calculating the density, volume,
pressure , radius of gyration and the Root Mean Square Deviation.

I would like to use vmd to view the molecule at the different times of the
simulation ( simulation lasted 80 picoseconds , and it was completed in
steps of 10ps) . However, I don`t have any trajectory output files so I am
not sure how to do this.

This is my sander code:

sander -O -i md1.in -o md1KCL.out -inf md1KCL.inf -c lr16wKCL.k.minw2 -ref
lr16wKCL.k.minw2 -r lr16wKCL.k.md1 -p lr16wKCL.k.top -x lr16wKCL.k.md1.x -e
lr16wKCL.md1.ene &

and the output files I get are:

lr16wKCL.k.md1, md1KCL.inf and md1KCL.out

I have also tried running the code by using lr16KCL.k.nc after -x but this
doesn’t work either.

I need lr16wKCL.k.md1.x in order to view the molecule in the vmd but for
some reason this code doesn’t output this trajectory file.

Unless, does the lr16wKCL.k.md1 output file contain the trajectory and can
I use this in lieu of the explicit trajectory file ?

many thanks,

Kris J Duna

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Received on Wed Jan 06 2021 - 05:00:02 PST
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