VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 06 2015 - 10:24:19 CST

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. 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.

http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/

> 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.

axel.

> Thanking you in advance..
> Dhritiman Talukdar
> dhritimant_at_gmail.com
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.