[AMBER] rotational diffusion error

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Mon, 30 Sep 2013 08:15:46 +0100 (BST)

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:


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


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.


Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
AMBER mailing list
Received on Mon Sep 30 2013 - 00:30:04 PDT
Custom Search