From: Geist, Norman (
Date: Mon Aug 29 2022 - 01:47:51 CDT

Best would be to see the content of your indexfile, probably the
format is just wrong ;)

Norman Geist

Am Freitag, den 26-08-2022 um 21:04 schrieb Efthymiou, Christos:

Hi Norman, 

I am trying to use catdcd on my Windows 10 computer using the commands
you provided but I am having some trouble. Here is the error that

>catdcd -s protein.pdb -o MD_protein.dcd -otype dcd -i indexfile -dcd
CatDCD 5.4
Reading indices from file 'indexfile'
Error opening index file indexfile Error reading index file.

I have tried renaming the index file in my folder to indexfile.txt and
indexfile.dat, but neither solved the issue. I also do not see .txt or
.dat listed as one of the accepted input file types for catdcd.
Therefore, what format should the index file be? Even without an
extension I got that same error message. 

Please let me know and thank you again for the help. 

From: Geist, Norman
Sent: Sunday, June 19, 2022 9:51 PM
To: Efthymiou, Christos ; Axel Kohlmeyer
Subject: Re: vmd-l: How to reduce the size of a .dcd file?

saving a shortened DCD is also quite easily possible. Load PSF and PDB
(PSF 1st.) and then in Extensions->TKConsole:

set a [atomselect top "not water"]
$a writepsf short.psf
$a writepdb short.pdb

Saving the indexfile for catdcd is similarly easy:

set fp [open indexfile w}]
set a [atomselect top "not water"]
puts $fp [$a get serial]
$a delete
close $fp

Then use catdcd like:

catdcd -s short.pdb -o short.dcd -otype dcd -i indexfile -dcd
long1.dcd -dcd long2.dcd 

Norman Geist

Am Sonntag, den 19-06-2022 um 15:15 schrieb Efthymiou, Christos:


Thank you for the link to the Windows installation! 

Reading the possible input files, I see that .psf files are not one of
the acceptable files. Is there a reason why water molecules cannot be
removed from psf files? For my particular case, I was interested in
using catdcd to reduce the size of my dcd trajectories to be able to
analyze them with the program MDContactCom, which requires dcd and psf
files as inputs. However, if I remove the water molecules from the dcd
file and not the psf file, I get this error: - Func: convert - ERROR - xyz must be shape (Any, 44191,
3). You supplied (200, 5508, 3)

Searching online, this seems to be caused by a disconnect between the
total number of atoms in the trajectory compared to the psf file (i.e.
the lack of water in the dcd file). Is there a way to remove water
molecules from the psf file? 

Thanks again for all the help. 

From: Axel Kohlmeyer
Sent: Friday, June 17, 2022 5:45 PM
To: Efthymiou, Christos
Cc: Geist, Norman ;
Subject: Re: vmd-l: How to reduce the size of a .dcd file?

 ⚠ Caution: External sender



On Fri, Jun 17, 2022 at 10:35 AM Efthymiou, Christos wrote:



Additionally, is catdcd available on Windows? I cannot find any
instructions or a manual on how to install and use the program. 



I have not installed VMD on Windows in a long time. It used to be that
a catdcd executable is only included in some packages and not in the
Windows package.
Quite some time ago for some tutorials (and my own education), I had
built Windows installer packages for catdcd. Those are still available
at:;!!DZ3fjg!4Gut2bYBTS5YLIwH3LACWcgrBY-Ln_yi40N5rw3PBrjnCaRpHusQmZZL9ZbuNwTCt5AJhHLc3dzDoDoDnjhYgcADk8dTBSlyWw$ [1]
Use at your own risk. I just checked with a Windows 11 virtual machine
and it can still be installed and run...


Microsoft Windows [Version 10.0.22000.739]
(c) Microsoft Corporation. All rights reserved.

CatDCD 5.4
   catdcd -o outputfile [-otype ] [-i indexfile]
      [-stype ] [-s structurefile]
      [-first firstframe] [-last lastframe] [-stride stride]
      [-] inputfile1 [-] inputfile2 ...

Allowed input file types:
crd crdbox XDATCAR rst7 OUTCAR xml vcf vtf js car dcd namdbin POSCAR
pqr cpmd dlpolyhist dlpoly3hist dlpolyconfig xyz tinker binpos ABINIT
pdb lammpstrj hoomd cor bgf xsf gro g96 trr trj xtc pdbx xbgf cube
mol2 dms dtr mae

Allowed output file types:
crd crdbox rst7 js dcd namdbin POSCAR pqr xyz binpos ABINIT pdb
lammpstrj hoomd bgf gro trr pdbx xbgf mol2 dms dtr mae



Thanks for the help!




Dr. Axel Kohlmeyer;!!DZ3fjg!4Gut2bYBTS5YLIwH3LACWcgrBY-Ln_yi40N5rw3PBrjnCaRpHusQmZZL9ZbuNwTCt5AJhHLc3dzDoDoDnjhYgcADk8eCQI4gMg$ [2]
College of Science & Technology, Temple University, Philadelphia PA,
International Centre for Theoretical Physics, Trieste. Italy.