Once again, it is more helpful to include your actual cpptraj output so
people can see exactly what you did. Often the problems are due to people
not actually doing what they thought they did.
On Wed, Aug 7, 2019, 6:57 AM Hira Jabeen <hira_bioinfo.yahoo.com> wrote:
> Hi Carlos,
> The commands were having same names in actual run as:
> parm 1m40_mem.prmtop
> trajin 1m40_mem.rst
> center :1-264 mass origin
> image familiar com :1-264
> outtraj 1m40_mem_image.rst ncrestart
> go
>
> Yes same prmtop file was used during md to generate rst file.
> Files are attached in separate mail.
> ThanksHira
>
> On Wednesday, August 7, 2019, 12:41:52 PM GMT+1, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> It's hard to help since the file names in the command list you gave don't
> match those in the output wih the error. Was that a different run?
>
> The error says your prmtop and rst file don't have the same number of
> atoms. That is pretty clear. Is this the same prmtop used to generate that
> restart during md?
>
> On Wed, Aug 7, 2019, 4:35 AM Hira Jabeen <hira_bioinfo.yahoo.com> wrote:
>
> > Hi Amber members,
> > I am using Amber 18 with AmberTools 19. I am trying to create an image
> > file of trajectory. The commands are as follow:
> > parm file_name.prmtop
> > trajin file_name.rst
> > center :1-264 mass origin
> > image familiar com :1-264
> > outtraj file_name_image.rst ncrestart
> > go
> > While using "autoimage" instead of "centre and image". I get the same
> > error with 'rst' file as:
> > CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.00)
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_| Date/time: 08/07/19 11:15:44
> > | Available memory: 60.273 GBINPUT: Reading input from 'image.in'
> > [parm 1m40_mem.prmtop]
> > Reading '1m40_mem.prmtop' as Amber Topology
> > Radius Set: modified Bondi radii (mbondi)
> > [trajin 1m40_mem.rst]
> > Reading '1m40_mem.rst' as Amber NC Restart
> > Error: Number of atoms in NetCDF file (26659) does not match number
> > Error: in associated topology (26643)!
> > Error: Could not set up '1m40_mem.rst' for reading.
> > Error: Could not set up input trajectory '1m40_mem.rst'.
> > 1 errors encountered reading input.
> > TIME: Total execution time: 0.1785 seconds.
> > Error: Error(s) occurred during execution.
> > Kindly suggest.
> > Thanks,Hira
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Aug 07 2019 - 06:30:02 PDT
