Thank you Dan for your reply.
By the way I still have some problem in getting the results.
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 [avg]
trajin $path/$system-reimage-set21.traj 1 1000
trajin $path/$system-reimage-set22.traj 1 1000
rotdif nvecs 1000 ref [avg] :DDM.C15,C16 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
But the data in file : deffs.dat is
1 0.00000000
2 0.00000000
3 0.00000000
4 0.00000000
5 0.00000000
6 0.00000000
7 0.00000000
8 0.00000000
9 0.00000000
10 0.00000000
11 0.00000000
12 0.00000000
13 0.00000000
14 0.00000000
.
.
.
1000 0.00000000
and data in the file: rotdif.out is
Results of small anisotropy (SVD) analysis:
Qxx Qyy Qzz Qxy Qyz Qxz
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
D_tensor
0.00000 -0.00000 -0.00000
-0.00000 0.00000 -0.00000
-0.00000 -0.00000 0.00000
D eigenvalues
0.00000 0.00000 0.00000
D eigenvectors (in columns)
1.00000 0.00000 0.00000
0.00000 1.00000 0.00000
0.00000 0.00000 1.00000
Dav, Daniso, Drhomb
0.00000 -nan -nan
taueff(obs) taueff(calc)
1 inf inf
2 inf inf
3 inf inf
4 inf inf
5 inf inf
6 inf inf
.
.
.
What is the error could be here? I can not trace the error.
Can I get some help here?
Many thanks in advance.
Regards
Vijay
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)
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Received on Tue Oct 01 2013 - 20:00:04 PDT
