VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Feb 19 2015 - 22:20:36 CST

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.