From: Francesco Pietra (
Date: Mon Sep 13 2021 - 04:58:30 CDT

Sorry for this untimely and naive post.

Actually, autopsf gen without patches was successful and I noticed that HIS
was assigned as HSD by default, which is acceptable for non protonated HIS.
Also. ILE CD1 -> CD by default.

On applying HS2 ASPP RN2 and LSN patches, Error: could not open "": no
such file or directory. The log file reads:
couldn't open "": no such file or directory
couldn't open "": no such file or directory
    while executing
"open $logfilename a"
    (procedure "::autopsf::makepatches_gui" line 13)
    invoked from within
    invoked from within
".autopsf.patches.finish invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .autopsf.patches.finish"
    (command bound to event)

I can't understand, not seeing any "" file anywhere.
Thanks for advice
francesco pietra

---------- Forwarded message ---------
From: Francesco Pietra <>
Date: Sat, Sep 11, 2021 at 4:21 PM
Subject: autopsf with many modifiers
To: VMD Mailing List <>

With protein-nucleic systems composed of a large number of subunits, the
use of autopsf avoids the burden required by the preparation of psfgen.
However, going on by trial and error (which is my case), resetting any time
all modifiers becomes more than annoying.

To this regard, should the same patch for different residues be specified
patch HS2 HIS:11H
patch HS2 HIS:243J
patch HS2 HIS:256J
patch HS2 HIS:259J
or can be combined in a single line?

Moreover, how to specify pdbalias (and, like above, could these be combined
in a single line for the same alias?):
pdbalias atom ILE CD1 CD
pdbalias residue HIS:209F HSE
pdbalias residue HIS:216G HSE
pdbalias residue HIS:218G HSE
pdbalias residue HIS:231J HSE
pdbalias residue HIS:133N HSE
pdbalias residue HIS:25P HSE
pdbalias residue HIS:28P HSE
pdbalias residue HIS:7Q HSE

regenerate angles dihedrals

Thanks a lot for advice
francesco pietra