VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 09 2010 - 16:42:53 CST
- Next message: Andrew: "Re: surface representation question"
- Previous message: John Stone: "Re: surface representation question"
- In reply to: Tristan Croll: "Bug in AutoIMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Andrew: "Re: surface representation question"
- Previous message: John Stone: "Re: surface representation question"
- In reply to: Tristan Croll: "Bug in AutoIMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]