As for adding to the previous email,
I have simulated for 300 ns. The trajectories are archived every 5 ps and I used time step dt=0.002. I generated 60 files with eachn file contain 1000 frames.
For testing purpose I use only 2 files (2000 frames)
I have calculated the rotational diffusion using command "rotdif nvecs 256 ref [avg] :DDM.C15,C16 ncorr 1200 ti 0.0 tf 2.4 dt 0.002 deffout deffs.dat itmax 5000 tol 0.000001 d0 0.03 order 2 outfile rotdif.dat"
But I get many warnings.
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 [avg]]
[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 256 ref [avg] :DDM.C15,C16 ncorr 1200 ti 0.0 tf 2.4 dt 0.002 deffout deffs.dat itmax 5000 tol 0.000001 d0 0.03 order 2 outfile rotdif.dat]
ROTDIF: Random seed 80531, # of random vectors to generate: 256
Max length to compute time correlation functions: 1200
Timestep = 0.0020, T0 = 0.0000, TF = 2.4000
Vector correlation functions will be calculated directly
Iterative solver: Max iterations = 5000, tol = 0.000001, initial guess = 0.030000
Order of Legendre polynomial = 2
Simplex scaling factor=0.5000
Deff will be written out to deffs.dat
Diffusion constants and tau will be written to rotdif.dat
PARAMETER FILES:
0: maltoLyo12per.top, 22224 atoms, 752 res, box: Orthogonal, 752 mol, 496 solvent, 2000 frames
INPUT TRAJECTORIES:
0: [maltoLyo12per-reimage-set21.traj] is an AMBER trajectory, Parm maltoLyo12per.top (Orthogonal box) (reading 1000 of 1000)
1: [maltoLyo12per-reimage-set22.traj] is an AMBER trajectory, Parm maltoLyo12per.top (Orthogonal box) (reading 1000 of 1000)
Coordinate processing will occur on 2000 frames.
REFERENCE COORDS:
The following 1 frames have been defined:
0: [avg] frame 1
Active reference frame for masks is 0
OUTPUT TRAJECTORIES:
No files.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [maltoLyo12per.top] (1 actions):
0: [rotdif nvecs 256 ref [avg] :DDM.C15,C16 ncorr 1200 ti 0.0 tf 2.4 dt 0.002 deffout deffs.dat itmax 5000 tol 0.000001 d0 0.03 order 2 outfile rotdif.dat]
ROTDIF: 512 atoms selected for RMS fit.
----- [maltoLyo12per-reimage-set21.traj] (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [maltoLyo12per-reimage-set22.traj] (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 2000 frames and processed 2000 frames.
ACTION OUTPUT:
ROTDIF:
256 vectors, 2000 rotation matrices.
Determining local diffusion constants for each vector.
0% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000090
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000062
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000094
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000056
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000075
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000081
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000091
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000094
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000084
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000062
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000084
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000067
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000077
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000055
10% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000063
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000054
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000058
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000094
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000088
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000065
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000055
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000093
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000081
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000053
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000065
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000055
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
20% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000065
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000069
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000059
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000076
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000069
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000075
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000079
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000075
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000054
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000071
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000059
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000066
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000084
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000062
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000079
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000064
30% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000081
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000059
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000069
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000064
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000091
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000076
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000056
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000060
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000076
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000089
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000079
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000057
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000071
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000089
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000088
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000071
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000057
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
40% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000088
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000093
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000090
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000084
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000079
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000063
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000054
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000088
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000066
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000057
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000077
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000059
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
50% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000065
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000065
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000071
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000077
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000057
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000060
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000066
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000055
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000091
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000066
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000081
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000063
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
60% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000069
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000062
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000090
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000081
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000069
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000069
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000086
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000079
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000089
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000091
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000064
70% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000071
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000065
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000084
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000067
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000084
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000062
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000077
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000075
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000057
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000091
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000079
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000059
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000070
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000058
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
80% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000063
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000063
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000075
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000056
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000082
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000081
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000067
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000074
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000063
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000060
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000059
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000069
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000079
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000067
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000066
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000071
90% Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000066
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000071
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000088
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000060
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000068
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000077
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000055
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000092
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000072
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000080
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000083
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000085
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000087
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000062
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000065
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000060
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000078
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000061
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000057
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000081
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000073
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000093
100% Complete.
Warning, itsolv did not converge: # iterations=5001, fractional change=0.000060
Determining diffusion tensor with small anisotropy.
Determining diffusion tensor with full anisotropy.
DATASETS:
No data sets.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
Can I get help on how to do this calculation using rotdif command in cpptraj especially to calculate rotational diffusion for specific site (exocyclic part) in glucose residue?
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, 1 October 2013, 5:49
Subject: Re: [AMBER] rotational diffusion error
Hi
On Mon, Sep 30, 2013 at 1:15 AM, Vijay Manickam Achari
<vjrajamany.yahoo.com> wrote:
>
> 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
>
> [rotdif nvecs 1000 ref .C15,C16,O16,H16 \ ]
In order for a line continuation to be valid there must be nothing
after the backslash character ('\'). In your case you have spaces
after '\', which is why cpptraj reads only the first line (which is
reported in the output). Remove the spaces after your backslashes.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 01 2013 - 21:30:03 PDT
