Fwd: Solved stream files and paratool

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Sep 23 2011 - 10:13:06 CDT


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

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

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.

francesco pietra

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