VMD-L Mailing List

From: Wasim Abdul (wasimorbrooklyn2013_at_gmail.com)
Date: Thu Jun 27 2019 - 09:10:46 CDT

I'm using Linux. I'll count the maximum number of bonds I have and let you
know. Thank you so so much.

On Thu 27 Jun, 2019, 7:39 PM John Stone, <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Axel's description is accurate.
>
> How many bonds do you actually need per-atom?
> If you're running Linux or MacOS, it is trivial for
> me to make a special build with a larger maximum bond count and post it
> for you. If you're using Windows, the process of making a special build
> is very involved and it would cost me too much time to be worth the
> trouble,
> and in that case I'd offer to build you a Linux version instead, as I'm
> sure you can find a machine to run it on. In any case, I would need to
> know
> how many bonds you actually need.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jun 27, 2019 at 08:31:22AM -0400, Axel Kohlmeyer wrote:
> > this number is a compile time choice. so to have a VMD executable
> with a
> > larger allowance for the number of bonds per atom, you need to
> compile a
> > custom executable, which is a non-trivial task unless you are familiar
> > with compiling software with many dependencies and unconventional
> build
> > scripts and settings. if you are running on windows and need a windows
> > executable, it is particularly challenging.
> > axel.
> > On Thu, Jun 27, 2019 at 8:25 AM Wasim Abdul
> > <[1]wasimorbrooklyn2013_at_gmail.com> wrote:
> >
> > I have the need to have many bonds per atoms as I want to visualize
> a
> > polymer network. I have used carbon as the atom name, but it is
> actually
> > a model system. I have a structure file ready, but VMD shows the
> errors
> > like the following for multiple atoms:
> > MolAtom 77: Exceeded maximum number of bonds (12)
> > Please help.
> >
> > --
> > Dr. Axel Kohlmeyer Ā [2]akohlmey_at_gmail.com Ā [3]http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA,
> USA
> > International Centre for Theoretical Physics, Trieste. Italy.
> >
> > References
> >
> > Visible links
> > 1. mailto:wasimorbrooklyn2013_at_gmail.com
> > 2. mailto:akohlmey_at_gmail.com
> > 3. http://goo.gl/1wk0
>
> --
> 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/
>