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
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| 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.
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Received on Sun Jun 12 2016 - 06:30:03 PDT
