What version of cpptraj are you using?
On Mon, Apr 25, 2016 at 6:54 AM, Jean-Patrick Francoia <
jeanpatrick.francoia.gmail.com> wrote:
> Thanks for your reply.
>
> > That's not an OpenDX file at all. What command did you use in cpptraj to
> > generate the .dx file?
>
> That makes sense then. I used the following command:
>
> volmap test_volmap 0.5 0.5 0.5 @* centermask @*
>
> But the doc clearly says:
>
> > volmap filename dx dy dz <mask> [xplor] [radscale <factor>] [ [[buffer
> > <buffer>] [centermask <mask>]] | [center <x,y,z>] [size <x,y,z>] ]
> > [peakcut <cutoff>] [peakfile <xyzfile>]
> > filename The name of the output file with the grid density. By default
> > it is written in the OpenDX file format
>
> Also, I get an error if I try to use the xplor key word (but then again,
> maybe I'm doing somethig wrong):
>
> volmap test_volmap 0.5 0.5 0.5 xplor @* centermask @*
> VOLMAP: Grid spacing will be 0.50x0.50x0.50 Angstroms
> Grid centered around @* with 3.00 Ang. clearance
> Density will wrtten to test_volmap
> Error: [volmap] Not all arguments handled: [ xplor ]
>
>
> Le 25/04/2016 12:14, Jason Swails a écrit :
> > On Mon, Apr 25, 2016 at 4:44 AM, Jean-Patrick Francoia <
> > jeanpatrick.francoia.gmail.com> wrote:
> >
> >> Hi,
> >>
> >> I generated an opendx file with the volmap command of cpptraj. VMD and
> >> Chimera are supposed to be able to read it, but it doesn't work.
> >> Chimera's error log says:
> >>
> >> Error reading file test_volmap.dx, format apbs
> >> Missing "object 1 class gridpositions counts <l> <m> <n>" header line
> >>
> >> Can I assume the opendx file outputed by volmap is not properly
> >> formatted ? Here is the head of the dx file:
> >>
> >> # VOLMAP_00000
> >> 1.000 1.000 1.000 0.0000
> >> 2.000 1.000 1.000 0.0000
> >> 3.000 1.000 1.000 0.0000
> >> 4.000 1.000 1.000 0.0000
> >> 5.000 1.000 1.000 0.0000
> >> 6.000 1.000 1.000 0.0000
> >> 7.000 1.000 1.000 0.0000
> >> 8.000 1.000 1.000 0.0000
> >> 9.000 1.000 1.000 0.0000
> >>
> > That's not an OpenDX file at all. What command did you use in cpptraj
> to
> > generate the .dx file?
> >
> >
> >> Could you tell me how I can visualize this map ?
> >>
> > It needs to be either an OpenDX or XPLOR grid file rather than a raw
> data
> > file with space-separated numbers.
> >
> > HTH,
> > Jason
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 25 2016 - 06:00:07 PDT
