Hi,
Looks to me like you specified "RO" (that's the letters 'R' and 'O')
as the rotation matrix data set name for your 'rotdif' command instead
of "R0" (that's the letter 'R' and the number zero).
-Dan
On Sun, Jun 12, 2016 at 11:44 PM, ATUL KUMAR <atul44_sit.jnu.ac.in> wrote:
> 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
>>
> _______________________________________________
> 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 Mon Jun 13 2016 - 08:00:03 PDT
