Only the first line of your 'rotdif' command is being processed (see
your output). The likely cause is whitespace after your backslash '\'
character. In order for backslash to continue a line, it must be the
final character on that line.
-Dan
On Sun, Jun 12, 2016 at 7:22 AM, ATUL KUMAR <atul44_sit.jnu.ac.in> wrote:
> Dear amber users, I am trying to calculate rotation diffusion of water
> molecules in my system. But I am getting following error
>
> CPPTRAJ: Trajectory Analysis. V15.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 06/12/16 18:26:54
> | Available memory: 38038.1 MB
>
> Reading 'DNA_Water.prmtop' as Amber Topology
> INPUT: Reading Input from file rotdif.in
> [trajin 1ns_wat1.nc]
> Reading '1ns_wat1.nc' as Amber NetCDF
> [reference wat_100ns1.rst]
> Reading 'wat_100ns1.rst' as Amber Restart
> [rms R0 .O reference savematrices]
> Reference mask: [.O](35381)
> RMSD: (.O), reference is "wat_100ns1.rst" (.O), with fitting.
> Rotation matrices will be saved to set 'R0[RM]'
> [rotdif rmatrix RO[RM] 10000 ref [avg] .O ]
> Error: 'dt <timestep>' must be specified and > 0.
> Error: Could not setup analysis [rotdif]
> 1 errors encountered reading input.
> TIME: Total execution time: 0.3883 seconds.
>
>
> The script I am using to calculate rotational diffusion is given below:
>
> trajin 1ns_wat1.nc
> reference wat_100ns1.rst
> rms R0 .O reference savematrices
> rotdif rmatrix RO[RM] 10000 ref [avg] .O \
> ncorr 5000 dt 0.001 ti 0.0 tf 1 deffout deffs.dat \
> itmax 100 tol 0.000001 d0 0.03 order 2 \
> outfile rotdif.out
>
> Please help me resolve this issue
>
> Thank you
> *Atul Kuamr jaiswal*
> Research Scholar
> School of Computational and Integrative Sciences
> Centre for Computational Biology and Bioinformatics (CCBB)
> JNU,New Delhi
> India.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Sun Jun 12 2016 - 09:00:02 PDT
