VMD-L Mailing List

From: Hugo Santos Silva (hsansilva_at_gmail.com)
Date: Sat Feb 21 2015 - 15:25:49 CST

Thank you very much, Axel

Both "issues" resolved.

Cheers,

Hugo

2015-02-20 5:20 GMT+01:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:

> On Thu, Feb 19, 2015 at 10:47 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> > On Thu, Feb 19, 2015 at 8:22 PM, Hugo Santos Silva <hsansilva_at_gmail.com>
> wrote:
> >> 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
> >> "noobness":
> >>
> >> 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
> >
> > that is incorrect syntax. topo addbond currently cannot add a bond
> > type or bond order.
>
> i should better read my own documentation carefully before answering.
> you *can* set the bond type. the syntax is:
>
> topo addbond 0 1 -bondtype BPENT
>
> nevertheless, if you want to override all bond types, using
> setbondlist is much more efficient.
>
> > the only want to do this would be to do:
> >
> > set blist { {0 1 BPENT} ... {0 18 BHEX} }
> > topo setbondlist type $blist
> >
> >> (...)
> >>
> >> topo retypeangles
> >
> > this has no effect since there are no angles defined yet.
> >
> >> topo addangle 0 1 2 APENT
> >> (...)
> >> topo addangle 1 0 18 AHEX
> >> (...)
> >
> > hmmm... looks that the documentation disagrees with the implementation.
> >
> >
> >>
> >> 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?
> >
> > bonds in VMD are handled (internally) differently than angles,
> > dihedrals and impropers, that has consequences on what topotools can
> > do.
> >
> >> 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
> >> rest.
> >> 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?
> >
> > that is not what the code is supposed to do. retyping means that all
> > existing impropers (or dihedrals or angles) are given a new type based
> > on the atom names. this somewhat follows the way how the CHARMM force
> > field assigns its force field parameters for bonded interactions. the
> > topology file (e.g. a .psf file) only contains the sequences of atoms
> > that make up those topology elements. there are no individual types
> > assigned. topo retypeXXX hence generates such initial type
> > assignments.
> >
> >
> > in short, your major problem is that you didn't pay enough attention
> > what the individual commands mean and what they are supposed to do and
> > not.
> >
> > axel.
> >
> >
> >>
> >> Thank you for your help
> >>
> >> Cheers,
> >>
> >> Hugo
> >>
> >> --
> >> __________________
> >> Hugo SANTOS SILVA, M. Sc.
> >> FP7-ITN Marie Curie PhD Fellow
> >> Équipe de Physique et Chimie des Polymères (EPCP) et de Chimie-Physique
> >> (ECP)
> >> 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
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> > International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
__________________
*Hugo *