a few suggestions:
1) don't convert to a pdb first, just load the restart directly into VMD
after loading the prmtop first.
2) if you're on windows, and saved your restart in netcdf format, then use
cpptraj to convert it to an ascii restart (give it a file extension of
.rst7).
On Thu, Nov 17, 2022 at 12:30 PM Kerry Woolnough via AMBER <
amber.ambermd.org> wrote:
>
> Hello,
>
> In Short:
>
> When attempting to load a prmtop and restart file into VMD, I am receiving
> the error “Mismatch between existing molecule or structure file atom count
> and coordinate or trajectory file atom count”, and I’m unsure of how this
> could arise.
>
> Long Version:
>
> I am new to MD and attempting to reproduce ambermd.org Tutorial 3.1
> (Relaxation of Explicit Water Systems) using pmemd.cuda and Amber20. The
> final relaxation stage is run with the following call:
>
> $AMBERHOME/bin/pmemd.cuda -O -i 9md.in\
> -o 9md.out -p RAMP1_ion.prmtop -c 8md.rst7 -r
> 9md.rst7\
> -inf 9md.info -ref 8md.rst7 -x mdcrd.9md
>
> In ‘Step 11. Checking Relaxation’, the instructions say to load the prmtop
> and then the rst7 files into a visualization program like VMD. I converted
> 9md.rst7 to PDB, loaded RAMP1_ion.prmtop into VMD as a new molecule,
> selected ‘Load Data into Molecule’, and chose my 9md_rst7.pdb file. I
> received an error stating that the files contain different numbers of atoms.
>
> To rule out unnoticed errors that may have occurred during my relaxation
> steps, I tried instead loading the prmtop and rst7 files downloaded
> directly from the succeeding tutorial (Tutorial 3.3 Running MD with Pmemd)
> but I encountered the same error:
>
>
> ERROR) Error reading optional structure information from coordinate file
> /Users /Downloads/VMD/RAMP1_equil_rst7.pdb
>
> ERROR) Will ignore structure information in this file.
>
> Info) Using plugin pdb for coordinates from file
> /Users/Downloads/VMD/RAMP1_equil_rst7.pdb
>
> ERROR) Incorrect number of atoms (17973) in
>
> ERROR) coordinate file /Users/Downloads/VMD/RAMP1_equil_rst7.pdb
>
> ERROR) Mismatch between existing molecule or structure file atom count and
> coordinate or trajectory file atom count.
>
> Info) Finished with coordinate file
> /Users/Downloads/VMD/RAMP1_equil_rst7.pdb.
>
> I’m unclear of how the restart file could contain a different number of
> atoms than the topology file used in the pmemd run that generated the
> restart file. If anyone could shed some light on this it would be greatly
> appreciated.
>
> Thanks!
>
>
>
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Received on Thu Nov 17 2022 - 10:00:03 PST
