VMD-L Mailing List
From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Jan 06 2015 - 13:32:09 CST
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.
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
> <mailto:akohlmey_at_gmail.com>> wrote:
> On Tue, Jan 6, 2015 at 10:36 AM, Dhritiman Talukdar
> <dhritimant_at_gmail.com <mailto: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.
> This limit
> > is coded into the program as a constant, but by a simple
> recompile, it can
> > be increased to an arbitrary number.
> what kind of a system do you have that requires more than 8 bonds *per
> atom*??? that is *very* unusual.
> since you have a "large system", it is more likely that your PDB file
> is actually not standard conforming and thus not readable except for a
> correct PDB reader
> PDB is not really a file format meant to be used for large system.
> better to use a more flexible file format.
> > Can somebody please recompile VMD with a higher limit say 50 or so..
> > I am using windows 7 32 bit OS.
> not likely going to happen unless you do it yourself.
> > Thanking you in advance..
> > Dhritiman Talukdar
> > dhritimant_at_gmail.com <mailto:dhritimant_at_gmail.com>
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> College of Science & Technology, Temple University, Philadelphia
> PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.