VMD-L Mailing List

From: John Grime (jgrime_at_uchicago.edu)
Date: Wed Oct 02 2013 - 16:45:14 CDT

Hello all,

I posted this message a couple of weeks ago, and there was no response at all, so I thought I'd repost it just in case it had fallen through the cracks and someone might see it and be able to help!

I'm trying to generate very large solvation boxes in VMD (v 1.9.1 for Linux on AMD64), and I have some problems.

Using the default segment prefix ("WT"), the solvation plugin runs until it tries to write the psf file, at which point it notices that the segid is longer than the 4 characters allowed in the PSF format and throws an error.

Changing the segment prefix to "W" seems to fix this, but there are then problems with the PSF plugin in VMD which produce error messages like this:

Info) Using plugin psf for structure file solvate.psf

psfplugin) ERROR: Bond 8351722 references atom with index < 1!

psfplugin) ERROR: skipping bond info due to bad atom indices

ERROR) Error reading bond information.

Is there a solution to this sort of issue? I'm trying to use the GUI version of VMD on a box with 64 GB of RAM, but if a command line solution exists then that's great!

Regards,

J.