[AMBER] Fwd: Desmond trajectory use with AMBER

From: D.A. Ragland <debra.ragland.gmail.com>
Date: Sun, 19 Oct 2014 14:26:28 -0400

Greetings,

I have been searching to find the answer to this question but I am afraid
that my question is a bit more specific than the answers I've been able to
find.

Recently, my PI has made me switch to using Desmond to run simulations.
Prior to the switch I was trained minimally on AMBER for simulations. I
have a few AMBER specific perl scripts to measure Ca-Ca distances of
trajectories (and RMSD, RMSF but I will not need these calculations) that I
would still like to use because they are familiar to me. I am aware that I
can load the Desmond trajectory into VMD to convert it into .top and .crd
files for use with AMBER, after converting the file to a DCD format.
However, I am not sure how to use the DCD file with my script (if this is
the trajectory file I am to use). I have attached the scripts for examining
if someone would be so kind.

The "debptr" script is used to generate ptraj files. After these files are
generated, I used to load the appropriate trajectory file into the correct
folder and then submit the "nwptr" file to the cluster for analysis. Once
the ptraj analysis was complete I would then run the "atom distance" script
to determine specific Ca distance pairs. I am wondering if I should
generate the .top and .crd using the leap feature and then place the DCD
file into the appropriate folder so that I may use these scripts?

I hope someone is able to help with this.

Thank you.

-- 
Debra Ragland
B.S. Chemistry
Ph.D. Candidate
UMass Medical School
Graduate School of Biomedical Sciences
Basic Biomedical Sciences Program
Schiffer Lab LRB 970M
-- 
Debra Ragland
B.S. Chemistry
Ph.D. Candidate
UMass Medical School
Graduate School of Biomedical Sciences
Basic Biomedical Sciences Program
Schiffer Lab LRB 970M



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Received on Sun Oct 19 2014 - 11:30:02 PDT
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