VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jun 23 2018 - 09:01:53 CDT

Adding that this is not a problem of path,as shown by th e extended command
below:

$ catdcd -o protein-GDP.dcd -i /home/francesco/trial_GBSA/index.in
> npt-05.pdb
> CatDCD 5.2
> Multiple plugins for file type 'off' found!Reading indices from file
> '/home/francesco/trial_GBSA/index.in'
> Error opening index file /home/francesco/trial_GBSA/index.in
> Error reading index file.
>

Rather, the question of "multiple plugins" is not clear to me.

fp

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sat, Jun 23, 2018 at 11:11 AM
Subject: catdcd error opening reading index file
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

With vmd 1.9.4a12, command

catdcd -o new.dcd -i index.ind my.dcd

reports error:
wrong # args: should be "catdcdList dcdFilename outFile indexFile stride"
as already posted by various users.

Setting catdcd5.2 on my path, the same command above, now from shell,
reports error:
catdcd error opening index.file
catdcd error reading index file

I was unable to find a list of catdcd errors, or any post dealing with such
error.

The index file, generated with the tcl script (in order to have the protein
and one of the ligands only, i.e. removing everything else)

set filename "index"
>
> #mol new npt-01.pdb type pdb waitfor all
> # set sel [atomselect top "((resid >=1 and resid <=426) or (resid >426 and
> <=502)"]
> set sel [atomselect top "segname PROB or segname GDPB"]
> # set indices [$sel get index]
>
> set file [open $filename.ind w]
> foreach indices [$sel get index] {
> puts $file "$indices"
> }
>
> # flush $file
> close $file
>

is zero based, as expected from vmd, and indexing is correct.

Thanks for advice

francesco pietra