VMD-L Mailing List

From: Dhritiman Talukdar (dhritimant_at_gmail.com)
Date: Wed Jan 07 2015 - 14:53:49 CST

Thanks to all..
I understood the problem with the pdb file..
When the number of atoms exceeds 6 digits the bonds section is written
incorrectly.
Dhritiman

On Wed, Jan 7, 2015 at 5:11 PM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:

> As others already pointed out, recompiling VMD will not solve your
> problem. What most likely happens when you load your PDB is, that is has a
> wrong format (notice that pdb is a fixed column format, not as many think
> columns separated by whitespace) so VMD doesn't correctly read the
> coordinates f.i. This causes many atoms to have the same positions which
> again causes many bonds between those atoms to be detected which are simply
> cutoff based. Your pdb is garbage, try recreating it.
>
> Another option which would actually bring up the same symptoms you see is
> if one takes a pdb and copies the content multiple times into the same
> file. Like a multi-frame pdb that misses the END lines to separate the
> frames. This would also cause many atoms to be at the same place and
> therefore are supposed to be bonded.
>
> You can also send me the PDB and I will check it.
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > Auftrag von Dhritiman Talukdar
> > Gesendet: Mittwoch, 7. Januar 2015 10:29
> > An: Axel Kohlmeyer
> > Cc: Vmd l; Josh Vermaas
> > Betreff: Re: vmd-l: Change bond per atom limit of VMD
> >
> > I am using RedHat 6.4 OS in Intel Cluster Studio
> > I tried to compile VMD 1.9.2 after editing Atom.h as it was suggested.
> > But I got the following message when I entered ./configure --help
> >
> > VMD plugin directory not found.
> > Please compile the VMD plugins and do 'make distrib' to copy them
> > into a 'plugins' directory linked or located in this directory.
> > Be sure your PLUGINDIR environment variable is set before running
> > 'make distrib' in the plugin build area.
> >
> > Please tell me how to compile the plugins.
> >
> > On Wed, Jan 7, 2015 at 12:51 PM, Dhritiman Talukdar
> > <dhritimant_at_gmail.com>
> > wrote:
> >
> > > I tried to save as mol2 file. but Avogadro was taking time.. I guess
> > there
> > > is no point in trying to convert the pdb to mol2 in OpenBable
> > although I
> > > tried it too..
> > > Please suggest any other file format I should try.
> > >
> > > Now about the force fields... For the smaller systems I have been
> > using
> > > the parameters form the following paper:
> > >
> > > 1. Interface of Grafted and Ungrafted Silica Nanoparticles with a
> > > Polystyrene Matrix: Atomistic Molecular Dynamics Simulations
> > > Tinashe V. M. Ndoro, Evangelos Voyiatzis, Azadeh Ghanbari, Doros
> > N.
> > > Theodorou, Michael C. Böhm, and Florian Müller-Plathe
> > > Macromolecules *2011* *44* (7), 2316-2327
> > > http://pubs.acs.org/doi/abs/10.1021/ma102833u
> > >
> > > pair_style lj/charmm/coul/charmm
> > > bond_style harmonic
> > > angle_style harmonic
> > > I have taken care of the units. I am using units style real
> > >
> > > On Wed, Jan 7, 2015 at 10:54 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> > > wrote:
> > >
> > >>
> > >> On Jan 7, 2015 5:41 AM, "Dhritiman Talukdar" <dhritimant_at_gmail.com>
> > >> wrote:
> > >> >
> > >> > I realize that none of the atoms should have more than 4 bonds in
> > the
> > >> structure and it doesn't.. But the total number of bonds is large so
> > maybe
> > >> that is the
> > >>
> > >> No, it isn't.
> > >>
> > >> problem. Also, I am having no problems with 32*32*32 file or lower.
> > After
> > >> using "topo retypebonds" and "topo bondtypenames", VMD shows only
> > Si-O bond.
> > >>
> > >> >
> > >> > The pdb file was made in Avogadro by adding a unit cell and then
> > using
> > >> Supercell Builder. Before saving the unit cell was removed.
> > >>
> > >> I repeat, it is a _very_ bad idea to use the pdb file format for
> > such a
> > >> large structure.
> > >>
> > >> >
> > >> > I will try with the Tersoff force field.
> > >>
> > >> I don't understand this statement. You will have to know which force
> > >> field you want to use _before_ you start building a topology and not
> > the
> > >> other way around.
> > >>
> > >> > Also automatic bond suppression by autobonds off filebonds off is
> > not
> > >> working in VMD text mode in a linux intel HPC.
> > >>
> > >> Nonsense. It works fine.
> > >>
> > >> >
> > >> > On Wed, Jan 7, 2015 at 1:53 AM, Axel Kohlmeyer
> > <akohlmey_at_gmail.com>
> > >> wrote:
> > >> >>
> > >> >>
> > >> >> On Jan 6, 2015 9:03 PM, "Josh Vermaas" <vermaas2_at_illinois.edu>
> > wrote:
> > >> >> >
> > >> >> > Hi Dhritiman,
> > >> >> > How was your pdb constructed? This system really shouldn't have
> > all
> > >> that many bonds (think about it, the lattice shouldn't have more
> > than 4
> > >> bonds per atom...), so I'd look more closely at how the system was
> > >> constructed rather than spend your time recompiling VMD.
> > >> >>
> > >> >> More importantly, if this is a malformatted pdb file, recompiling
> > vmd
> > >> will not solve anything. Vmd won't complain, but the structure will
> > be
> > >> garbage.
> > >> >>
> > >> >> Also, for some SiO2 force fields that lammps supports (e.g.
> > Tersoff),
> > >> there must not be bonds in the.topology and thus automatic bond
> > generation
> > >> must be suppressed.
> > >> >>
> > >> >> > -Josh Vermaas
> > >> >> >
> > >> >> >
> > >> >> > On 01/06/2015 12:15 PM, Dhritiman Talukdar wrote:
> > >> >> >>
> > >> >> >> The system I am referring to is a 37*37*37 Silica Cube. (37
> > being
> > >> the number of SiO2 i.e. 37 Si and 74 O).
> > >> >> >> I need it for finally making a spherical silica nanoparticle.
> > The
> > >> sphere will be sculpted out using LAMMPS.
> > >> >> >> I will compile VMD in Linux. May be it will be easier there.
> > >> >> >>
> > >> >> >> On Tue, Jan 6, 2015 at 9:54 PM, Axel Kohlmeyer
> > <akohlmey_at_gmail.com>
> > >> wrote:
> > >> >> >>>
> > >> >> >>> On Tue, Jan 6, 2015 at 10:36 AM, Dhritiman Talukdar
> > >> >> >>> <dhritimant_at_gmail.com> wrote:
> > >> >> >>> > Hi,
> > >> >> >>> > I need to load a large pdb file in VMD. when I try it VMD
> > gives
> > >> the
> > >> >> >>> > following error:
> > >> >> >>> >
> > >> >> >>> > MolAtom xxxx: Exceeded maximum number of bonds
> > >> >> >>> >
> > >> >> >>> > I have learned that the VMD provides space for 8 bonds per
> > atom=
>
>
>