VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 28 2011 - 05:44:13 CDT

On Sep 28, 2011, at 3:44 AM, "JhonY. I." <yijhon_at_hotmail.com> wrote:

> In win32 VMD, I've got the following error message.
>
> ERROR) BaseMolecule: Cannot add atom; namelist index value too large.
> ERROR) Recompile VMD with larger index types.
> ERROR) Atom namelist index values at time of overflow:
> ERROR) nameindex: 32768
> ERROR) typeindex: 0
> ERROR) resnameindex: 0
> ERROR) segnameindex: 0
> ERROR) altlocindex: 0
> ERROR) chainindex: 0
> ERROR) MolFilePlugin: file load aborted
> ERROR) molecule_structure: Unable to read structure for molecule 0
> ERROR) molecule_structure: severe error indicated by plugin aborting loading of
> molecule 0

What file format is this with? And what version of VMD? The error
message indicates that you are doing something stupid like giving
every atom a different name. It is the list of named that is
overflowing, not the number of atoms.

>
> I've downloaded source files followng the message of "Recompile VMD with larger index types."
> However, I don't know what index I should change in the source files and how I compile the files in windows XP system.

Compiling VMD in windows requires a lot of experience. Also the change
that you have to make is far from trivial since these indes numbers
are stored as short integers.

> Would you let me know of them in detail or where I can get the guide file for it?

Have you compiled software on windows before ?
There is developer information on the VMD home page.

Axel

>
> Thanks for the helps in advance.
>
> Young
>
>