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From: Vijay Manickam Achari <vjrajamany.yahoo.com>

Date: Wed, 2 Oct 2013 05:09:34 +0100 (BST)

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

Date: Wed, 2 Oct 2013 05:09:34 +0100 (BST)

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

___ ___ ___ ___

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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:

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/amberReceived on Tue Oct 01 2013 - 21:30:03 PDT

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