Re: [AMBER] Imaging-rst file error

From: Hira Jabeen <hira_bioinfo.yahoo.com>
Date: Wed, 7 Aug 2019 13:51:30 +0000 (UTC)

 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Aug 07 2019 - 07:00:03 PDT
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