Tutorial-l Mailing List

From: María Pedrosa (mpedrosab_at_gmail.com)
Date: Sun Dec 27 2020 - 17:21:36 CST

Dear all,
I am following the RBCG tutorial but I get to step 8 in section 1.2 (i.e
correct the protein segments in the PSF file) and write the commands

source fix_martini_psf.tcl
fix_martini_psf 0 martini-protein.top
01-CG-lipoprotein_autopsf.psf 01-CG-lipoprotein_autopsf.pdb CG-
fix_martini_psf 1 ../05-scripts 1 -1

in the TkConsole the following error appears:

"couldn't execute " ../05-scripts/dsspcmbi": no such file or directory"

I have tried copying the dsspcmbi file in the same folder as the tcl file,
but it still shows the same error.

I have discovered that if I change line 213 of the fix_martini_psf.tcl
file from:

  set dsspstream [open "| [file join ${dssppath} dsspcmbi] -v $pdbfile"]

to

  set dsspstream [open "dsspcmbi"]

and place the dsspcmbi file in the same folder, it finds it but the output
is not correct.

I would appreciate some help with this problem.
Thank you in advance,
María

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