From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Sep 23 2011 - 10:12:04 CDT

Solved the issue of ptl files.
fp

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Fri, Sep 23, 2011 at 1:00 PM
Subject: Fwd: vmd-l: Saved project and paratool
To: vmd-l_at_ks.uiuc.edu

Appended stream data to rtf let Paratool read/interpret them.

However, as the procedure is quite long, I tried to save the project
at an intermediate stage as internal ptl file.
Although Paratool collects the data for my cluster, it is unable to
open the saved file;

Cannot find molecule 0 in atomselect's 'molId'
Cannot find molecule 0 in atomselect's 'molId'
   while executing
"atomselect $molidbase "index $index""
   (procedure "set_atomprop" line 21)
   invoked from within
"set_atomprop Charge $i [get_atomprop Charge $i]"
   (procedure "load_project" line 83)
   invoked from within
"load_project $file"
   (procedure "::Paratool::opendialog" line 98)
   invoked from within
"::Paratool::opendialog loadproject"
   invoked from within
".paratool.#paratool#menu.#paratool#menu#file invoke active"
   ("uplevel" body line 1)
   invoked from within
"uplevel #0 [list $w invoke active]"
   (procedure "tk::MenuInvoke" line 50)
   invoked from within
"tk::MenuInvoke .paratool.#paratool#menu.#paratool#menu#file 1"
   (command bound to event)

Does that contain enough information to give hints as to what is going wrong?

Thanks

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Fri, Sep 23, 2011 at 10:10 AM
Subject: vmd-l: stream files and paratool
To: vmd-l_at_ks.uiuc.edu, NAMD <namd-l_at_ks.uiuc.edu>

Hello:
Currently both VMD and NAMD have been made capable of
reading/interpreting CHARMM str files. As far as I understand, this is
not the case of plugin Paratool. I tried by renaming str to either rtf
or prm but it seems to be a wrong way.

What I did follows. I am trying to parameterize a metal cluster by
simplifying the organic ligands as a piece of the corresponding aa in
the protein (for ex imidazole for HIS). I renamed the imidazole atoms
in my cluster to match the names in imidazole of the str file. When I
go to edit atoms in Paratool by pressing "Choose Type", it is not the
str (or rtf renamed) file that it is checked. Rather, Univ FF atom
types are presented, as if there were no topology/parameter files
added.

Is it any simple modification of the original str file so as it is
read as  if it were rtf? Or the only practical way is to append the
str file to the main rtf?(I did not try the latter)

If it is as above described, could Paratool - even if currently
lacking a developer - be made capable of reading str files? I mean by
expert developers did so for VMD/NAMD.

Thanks
francesco pietra