VMD-L Mailing List

From: Geist, Norman (norman.geist_at_uni-greifswald.de)
Date: Mon Aug 29 2022 - 04:07:18 CDT

Hi,

I think the indexfiles catdcd expects should be 0-indexed, not
1-indexed. Simply do:

puts $fp [$a get index]

instead of

puts $fp [$a get serial]

and it should work.

You can also add "-nonewline" to TCL's puts to prevent the final
"additional" linebreak.

Bests
Norman Geist

Am Montag, den 29-08-2022 um 10:55 schrieb Efthymiou, Christos:

Dear Norman, 

 
I checked the index file, and the error seems to have been caused by a
second blank line in the index file that needed to be deleted.
However, now another error has appeared: 

 
>catdcd -s protein.pdb -o MD_protein.dcd -otype dcd -i indexfile -dcd
MD.dcd
CatDCD 5.4
Reading indices from file 'indexfile' Atom index #6622 (6623) is out
of range.
 

 
If I load the protein.pdb file into VMD, it shows there are 6623
atoms, therefore I do not understand how atom index #6622 (6623) can
be out of range. My index file formatting is the following: 

 
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 ... 6618 6619 6620 6621 6622 6623
 

 
And the index file was created with slightly modifying the tcl code
you provided: 

 
set fp [open indexfile w]

set a [atomselect top "protein"]
puts $fp [$a get serial]
$a delete
close $fp
 

 
Please let me know if you have any ideas for solving this error. 

 
Best, 
Christos 

 

 
 
-------------------------
 
From: Geist, Norman
Sent: Monday, August 29, 2022 9:47 AM
To: Efthymiou, Christos ; Axel Kohlmeyer
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: How to reduce the size of a .dcd file?
 
Best would be to see the content of your indexfile, probably the
format is just wrong ;)

Bests
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
appears: 

 
>catdcd -s protein.pdb -o MD_protein.dcd -otype dcd -i indexfile -dcd
MD.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. 

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

 
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 

 
Bests
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: 

 
traj2pdb.py - 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. 

 
Best, 
Christos 
 
-------------------------
 
From: Axel Kohlmeyer
Sent: Friday, June 17, 2022 5:45 PM
To: Efthymiou, Christos
Cc: Geist, Norman ; vmd-l_at_ks.uiuc.edu
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: https://urldefense.com/v3/__https://rpm.lammps.org/windows/testing/__;!!DZ3fjg!7xdz7-NHCdt4GsH529ulLEDNMsiOokF5OPWiibmlsqmOpeEhKsK3e6QVQ4TzDKq1moScjgsIv11F35T6OYjhgMULhrPG93aFug$ [1]
Use at your own risk. I just checked with a Windows 11 virtual machine
and it can still be installed and run...

 
Axel.

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

C:\Users\akohl>catdcd
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!

 
Best, 
Christos 

 

  --

Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!7xdz7-NHCdt4GsH529ulLEDNMsiOokF5OPWiibmlsqmOpeEhKsK3e6QVQ4TzDKq1moScjgsIv11F35T6OYjhgMULhrPHfi9GKA$ [2]
College of Science & Technology, Temple University, Philadelphia PA,
USA
International Centre for Theoretical Physics, Trieste. Italy.

    

  

Links:
------
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[2]
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