VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 17 2002 - 09:55:15 CDT

Dear Jeff,
  We had hoped to have an Amber 7 plugin for VMD written already, but
for various reasons it has taken much longer than originally anticipated.
One of the VMD users has volunteered to take on this effort, but I'm
willing to do it myself if there's not progress on it by the time I
return from Siggraph at the end next week. In principle we should
be able to take the recently updated Amber 7 code in NAMD and make
it a VMD plugin, and we'd be in business, but nobody has been able to
get this done yet. Worst case I'll take the code with me on my laptop
and see if I can work on it while I'm out of town next week. That'll
give me something to do while sitting in the airport on the way back
too...

  John

On Wed, Jul 17, 2002 at 02:51:49AM -0400, Jeff Ames wrote:
> Hello --
>
> I'm trying to read in a parm and crd set from AMBER 7, in VMD 1.7.1 under
> Linux. But VMD seems to choke on the parm file, saying "not equipped to
> read perturbation prmtop". From the code (parm.c) it seems like it's
> reading the ifpert value of the parm file as being nonzero, though from
> looking at the parm file, it looks like it should be 0....
>
> The POINTERS section of my parm file is as follows (spaces adjusted so
> it'll fit on a single line):
>
> %FLAG POINTERS
> %FORMAT(10I8)
> 11183 17 10761 452 554 694 946 1128 0 0
> 17598 3547 452 694 1128 34 59 31 27 1
> 0 0 0 0 0 0 0 1 33 0
> 0
>
> I believe the first number on the third line is the ifpert value (0).
> I've tried setting every number here to 0 (simultaneously), and I've
> gotten the same error, so it seems that VMD is getting completely confused
> about the file somewhere. It's an AMBER 7 format file, and starts off
> with %VERSION. If it does determine the version correctly (anyone know
> how to see the iout stream output?), then it's also doing all the
> moveto()'s right, as it doesn't leave that function before the ifpert
> check. So I'm not sure what's going wrong here.
>
> I've also tried VMD 1.8a16, but it crashes when I try to open the parm/crd
> files, with no output.
>
> Any ideas? I can provide the full files I'm using if it'd help.
>
> TIA,
> Jeff 

-- 
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