VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jan 07 2015 - 05:41:11 CST

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=