From: Hugo Santos Silva (
Date: Thu Feb 19 2015 - 19:22:44 CST

Dear all,

In a week time, I've got to know Lammps, followed Axel Kohlmeyer's
beautiful tutorial on topotools and finally got some nice topologies
running for tests. thank you!

However, I indeed have two issues that probably are due only to my

1 - I'm trying to create a C60 topology using topotools. All the carbons
are equal (called them CFUL) but there are two different bond types.

After loading the pdb file, my tcl script looks like this>

set selc [atomselect top {name C}]
$selc set type CFUL
$selc set mass 12.01100
$selc set charge 0.000 ;
set sel [atomselect top all]

topo retypebonds
topo addbond 0 1 BPENT
topo addbond 0 18 BHEX

topo retypeangles
topo addangle 0 1 2 APENT
topo addangle 1 0 18 AHEX

topo retypedihedrals
topo adddihedral 0 1 2 14 DIHED

the issue arises from the fact that topotools can recognize the angletypes
as APENT and AHEX, for example, but not the bonds! no matter what I do (mol
bondsrecalc top, mol reanalyze top), when I ask bondtypenames, it lists me
90 different bond types CXX-CYY instead of listing 2, BPENT and BHEX, as it
does for angles. any clue on this, please?

2 - yesterday I was trying to input some impropers for a given traditional
molecule with CA, HA, CT and HC atom types. the bonds and angles were
nicely recognized.
it guessed lots of dihedrals and I just wanted one of them. i deleted the
but, for impropers, as it should be, vmd's guess was not perfect. then,
instead of adding all of them by hand, I would expect that typing topo
retypeimpropers CA-CA-CT-HC, I would have all the impropers formed by
these atoms indexes listed and added. instead, topotools just ignored me.
again, any clue on what I'm doing wrong?

Thank you for your help




*​​Hugo SANTOS SILVA, M. Sc.*
*FP7-ITN Marie Curie PhD Fellow*
Équipe de Physique et Chimie des Polymères (EPCP) et de Chimie-Physique
Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement
et les Matériaux - IPREM
Université de Pau et des Pays de l'Adour - UPPA
2 rue du Psdt. Pierre Angot, 64053, Pau Cedex, France
+33(0)559407996 (bureau) / +33(0)622151308 (portable)
Fachbereich Chemie - Institut für Physikalische und Theoretische Chemie
Eberhard Karls Universität Tübingen
Auf der Morgenstelle 18, 72076 Tübingen, Deutschland
Handy: +49(0)176/35039713