From: Tristan Croll (
Date: Sun Dec 05 2010 - 19:42:50 CST


I seem to have come across a little bug in AutoIMD that crops up when trying to run on a sub-selection of a solvated and ionized protein. When trying to connect to NAMD, it sometimes times out with the error "Reason: FATAL ERROR: DIDN'T FIND "NATOM" IN PSF FILE autoimd.psf". Checking the autoimd.psf file in my particular case, I found it had mis-counted the remarks by 1 - ie. it had:

      17 !NTITLE

Followed by only 16 REMARKS lines.

It only happens sometimes, but I think I've found a pattern - it only seems to occur where my overall construct is ionized, but the selection I want to run IMD on doesn't happen to contain any ions.

Hope this is useful.