From: Dhritiman Talukdar (dhritimant_at_gmail.com)
Date: Mon Jan 12 2015 - 13:40:49 CST

Hi,
No.. I am not recompiling VMD. I understood that .pdb is a column specific
format and the number of digits in the number of atoms in the pdb file
exceeded the number of columns specified for atom IDs. Hence the pdb file
was garbage.

On Mon, Jan 12, 2015 at 10:10 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I'm not sure if your problem is resolved or not, but as others have
> indicated, recompiling VMD seems unnecessary. That said, if you insist
> on pushing ahead with recompiling VMD, you would be well served to read the
> documentation on compiling VMD from source code:
> http://www.ks.uiuc.edu/Research/vmd/doxygen/
> http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html#compiling
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jan 07, 2015 at 02:58:37PM +0530, Dhritiman Talukdar wrote:
> > 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. Bo??hm, and Florian Mu??ller-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
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>