Hi AMBER users,
I intend to calculate average distance matrix between residues within a
trajectory containing 10000 frames. I found out that I can use matrix
command within the cpptraj. I wrote a script which contains the following
lines for the analysis:
*cpptraj mysystem.prmtop << EOFtrajin remd.TEMP.298.00rms first .CAmatrix
dist .CA out dist_avg.gnuquitEOF*
I saved the file as inter_residue_dis_avg.sh and then tried to run from the
terminal.
----------------------------
CPPTRAJ: Trajectory Analysis. V12.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> [trajin remd.TEMP.298.00]
[remd.TEMP.298.00] contains 10000 frames.
> [rms first .CA]
> [matrix dist .CA out dist_avg.gnu]
>
----------------------------------
I get the above output in the terminal but *dist_avg.gnu* file is not
written.
Could anyone point out what am I doing wrong or how to calculate the
distance.
With regards,
--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Mon Jul 14 2014 - 05:00:02 PDT
