From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 09 2010 - 16:42:53 CST

Hi,
  I'll need to see the full PSF files and the steps you used to create
them in order to be able to track down which tool might have done something
incorrect in generating the PSF file(s) that have been giving you trouble.
Can you provide that information to us?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 06, 2010 at 01:44:48PM +1000, Tristan Croll wrote:
>
>
> Hi,
>
>
>
> First, my apologies if this posts twice. I've just subscribed to the
> list, but haven't seen my first sending of this come up.
>
>
>
> 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.
>
>
>
> Cheers,
>
>
>
> Tristan
>
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078