VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Tue Mar 07 2023 - 16:47:47 CST

Hello,

I have created a tcl script and I am trying to run it on a supercomputer. Here is the script:

---------------
# Load psf file so you can create a new psf file with just the protein

mol new Full.psf type psf
mol new Full.pdb type pdb

set a [atomselect top "protein"]
$a writepsf protein.psf
$a writepdb protein.pdb

set fp [open indexfile w]
set a [atomselect top "protein"]
puts $fp [$a get index] nonewline
$a delete
close $fp

mol delete 0
mol delete 1

catdcd -o MD_10_stride_protein.dcd -otype dcd -i indexfile -dcd MD.dcd -stride 10
---------------------------------

When I check the output of the run, I see the following:

-----------------------------------
Info) Finished with coordinate file Full.pdb.
atomselect0
psfplugin) WARNING: PSF file is incomplete, no angles, dihedrals,
psfplugin) impropers, or cross-terms will be written.
Info) Opened coordinate file protein.psf for writing.
Info) Finished with coordinate file protein.psf.
Info) Opened coordinate file protein.pdb for writing.
Info) Finished with coordinate file protein.pdb.
file4
atomselect1
No plugin found for filetype 'stride'
CatDCD 5.1
Reading indices from file 'indexfile'
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opening file 'MD_10_stride_protein.dcd' for writing.
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opened file 'MD.dcd' for reading.
Read 50000 frames from file MD.dcd, wrote 50000.
----------------------------

Therefore, everything seems to be working properly except for the error "No plugin found for filetype 'stride'". Does this mean that the catdcd installed on the supercomputer is not capable of setting a stride? I can't find a mistake in the catdcd command in my script, so I am not sure why this is happening.

Best,
Christos