Thank you Dan for reply. I removed blank space after '\' but now I am
getting the following error:
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 06/13/16 10:49:51
| Available memory: 37969.5 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 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]
Error: Must specify data set containing rotation matrices.
Error: These can be generated with the 'rms' command and the 'savematrices'
Error: keyword. The resulting data set has aspect [RM], e.g.:
rms R0 .CA reference savematrices
rotdif rmatrix R0[RM] ...
Error: Could not setup analysis [rotdif]
1 errors encountered reading input.
TIME: Total execution time: 0.3923 seconds.
The new ptraj script 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 out with this. Thank you.
*Atul Kuamr jaiswal*
Research Scholar
School of Computational and Integrative Sciences
Centre for Computational Biology and Bioinformatics (CCBB)
JNU,New Delhi
India.
On Sun, Jun 12, 2016 at 9:14 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jun 12 2016 - 23:00:03 PDT
