Hi,
This problem usually occurs when the topology you are using does not
match the trajectory. The name of your trajectory leads me to believe
it has been stripped of waters. If this is the case you also need to
use a stripped topology, which can be obtained via the
'strip'/'parmstrip' commands in cpptraj or the 'strip' command in
parmed.
Hope this helps,
-Dan
On Fri, Feb 26, 2016 at 3:38 AM, Sivanandam M <sivanandamphy.gmail.com> wrote:
> Dear AMBER users,
> I analysed one MD trajectory file using
> CPPTRAJ module. That job gives the following error. Please advice me to
> rectify this problem.
>
>
>
> CPPTRAJ: Trajectory Analysis. V14.25
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> Reading 'c1-lig.prmtop' as Amber Topology
> INPUT: Reading Input from file strip3.in
> [trajin prod_dry.mdcrd]
> Reading 'prod_dry.mdcrd' as Amber Trajectory
> Error: In prod_dry.mdcrd, expect only 3 or 6 box coords, got 5
> Error: Box line=[ 54.051 32.808 49.526 54.909 33.095
> ]
> Error: Could not set up prod_dry.mdcrd for reading.
> Error: Could not set up input trajectory 'prod_dry.mdcrd'.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.4008 seconds.
>
> --------------------------------------------------------
> M.SIVANANDAM
> Research Scholar
> Department of Physics
> School of Physical Sciences
> Periyar University
> Salem-636 011
> Mobile- 9965582730, 9042066076
> --------------------------------------------------------
> _______________________________________________
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> 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 Fri Feb 26 2016 - 07:30:04 PST
