Dear Amber users,
I am trying to calculate the rotational diffusion for exocyclic group for sugar units where the sugars are arranged in a bilayer structure.
I used the command as below:
system="maltoLyo12per"
path="/home/vijay/Simulation-Folder-Feb2013/chapter6-lyo-paper1-Vj/trajmalto12per"
top="$path/$system.top"
cpptraj $top << EOF
reference $path/maltoLyo12per-reimage-set21.traj.pdb.1
trajin $path/$system-reimage-set21.traj 1 1000
trajin $path/$system-reimage-set22.traj 1 1000
rotdif nvecs 1000 ref .C15,C16,O16,H16 \
ncorr 90 ti 0.0 tf 0.80 dt 0.002 deffout deffs.dat \
itmax 500 tol 0.000001 d0 0.03 order 2 \
outfile rotdif.out
EOF
At some parts, I follow as described in AmberTools13, page 259. But unfortunately I am getting error message as below:
CPPTRAJ: Trajectory Analysis. V13.15
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
INPUT: Reading Input from STDIN
[reference /home/vijay/Simulation-Folder-Feb2013/chapter6-lyo-paper1-Vj/trajmalto12per/maltoLyo12per-reimage-set21.traj.pdb.1]
[maltoLyo12per-reimage-set21.traj.pdb.1] contains 1 frames.
[maltoLyo12per-reimage-set21.traj.pdb.1] is a PDB file, Parm maltoLyo12per.top (reading 1 of 1)
[trajin /home/vijay/Simulation-Folder-Feb2013/chapter6-lyo-paper1-Vj/trajmalto12per/maltoLyo12per-reimage-set21.traj 1 1000]
[maltoLyo12per-reimage-set21.traj] contains 1000 frames.
[trajin /home/vijay/Simulation-Folder-Feb2013/chapter6-lyo-paper1-Vj/trajmalto12per/maltoLyo12per-reimage-set22.traj 1 1000]
[maltoLyo12per-reimage-set22.traj] contains 1000 frames.
[rotdif nvecs 1000 ref .C15,C16,O16,H16 \ ]
Error: Rotdif: 'dt <timestep>' must be specified and > 0.
Error: Could not initialize action [rotdif]
In the command I already defined the "dt" value. But still I get error. I am not sure where I went wrong or what corretion need to be done. Could anyone help me please ?
Many thanks in advance.
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Mon Sep 30 2013 - 00:30:04 PDT
