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
