Hi,
Thanks for the topology file. There is indeed a # of atoms mismatch
between the topology (26643) and the restart (26659). This topology
can't be the one that was used to generate/ was created with this
restart file. If you try to run a simulation with the given topology
and coords you'll also get a # atoms mismatch error. How exactly were
both of these files generated?
-Dan
On Wed, Aug 7, 2019 at 9:51 AM Hira Jabeen <hira_bioinfo.yahoo.com> wrote:
>
> Hi Carlos,
> Apologies for not being clear.
> Actually in my system, ligand is drifting away during initial nanoseconds of MD runs, I applied some restraints but not working. According to suggestions, another way is to use "image with centre" through cpptraj. I am trying to generate image file after every 10ns chunks during entire simulation run (500ns).But here I am stucked with this error of (not same number of atoms) of prmtop and rst (which is weird!) as the same prmtop file was used to generate rst during MD.
> The input for imaging is:
> 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
> While the full cpptraj output is:
> CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.00)
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_| Date/time: 08/07/19 14:31:25
> | Available memory: 33.831 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: 0.0696 seconds.
> Error: Error(s) occurred during execution.
> rst file is attached here with while prmtop is about 5.2Mb cant upload.
>
> Best regards,HiraPhD Student in Computational ChemistryCentre for Computational ChemistrySchool of ChemistryUniversity of BristolCantock's CloseBristol BS8 1TS
> On Wednesday, August 7, 2019, 02:20:37 PM GMT+1, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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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Received on Thu Aug 08 2019 - 11:00:02 PDT
