VMD-L Mailing List

From: Martin Jones (mkjones_at_uabmc.edu)
Date: Fri May 24 2013 - 14:02:50 CDT

The situs file is not there. Nothing is logged in the VMD DOS Window after volmap.

What program is supposed to run next?

-----Original Message-----
From: Ryan McGreevy [mailto:ryanmcgreevy_at_ks.uiuc.edu]
Sent: Friday, May 24, 2013 1:42 PM
To: Martin Jones
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: MDFF difficulties with mdff sim command

That .dx file is just a temporary file VMD creates before blurring it to the appropriate resolution and writing out the final file which is the 4ake-target_autopsf.situs. Check your current VMD working directory for the 4ake-target_autopsf.situs file.

Martin Jones wrote:
>
> Hello,
>
> I have started the MDFF tutorial, using VMD for WIN32 1.9.1 on Windows
> 7 (64 bit). The MDFF is version 0.2.
>
> When I issue the following command on page 9
>
> mdff sim $sel -res 5 -o 4ake-target_autopsf.situs
>
> Instead of a situs file, a dx file is created, e.g.
>
> mdff_sim5932482353380174.dx
>
> The first few lines of which is:
>
> # Data calculated by the VMD volmap function
>
> object 1 class gridpositions counts 43 61 57
>
> origin -22.5 -34.5 -38.5
>
> delta 1 0 0
>
> delta 0 1 0
>
> delta 0 0 1
>
> ...
>
> And the DOS window also reports (a different attempt is shown):
>
> Info) volmap: Computing bounding box coordinates
>
> Info) volmap: grid minmax = {-23 -35 -39} {20 26 18}
>
> Info) volmap: grid size = 43x61x57 (0.6 MB)
>
> Info) volmap: writing file "c:mdff_sim5816507840443639.dx".
>
> Any help would be appreciated!
>
> Thanks,
>
> Martin
>
> ______________________________
>
> _ _
>
> Martin K. Jones
>
> University of Alabama at Birmingham
>