Hi,
The documentation for 'volmap' is a bit out of date. The format of the
output file can be chosen by given your output file a different
extension: for OpenDX use '.dx', for Xplor use '.xplor', etc (similar
to output from 'grid').
-Dan
On Mon, Apr 25, 2016 at 7:12 AM, Jean-Patrick Francoia
<jeanpatrick.francoia.gmail.com> wrote:
> I'm using:
>
> CPPTRAJ: Trajectory Analysis. V15.00
>
> Le 25/04/2016 14:53, Jason Swails a écrit :
>> 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
>>>>
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Apr 25 2016 - 08:00:03 PDT
