It will help if you could provide your exact cpptraj input, and maybe
some details about your system.
That said, you can adjust the isovalue in VMD to view different
contouring levels. ~1e-05 seems good to me.
-Dan
On Mon, Apr 25, 2016 at 1:26 PM, Jean-Patrick Francoia
<jeanpatrick.francoia.gmail.com> wrote:
> Ok, now it works. I can open the file in VMD or chimera.
> I just have a little problem now: nothing appears when I open the file .dx.
>
> I looked inside the file, and I only see very small numbers. I attached my
> dx file. Could you have a look and tell me if something went wrong please ?
>
> Sincerely
>
>
> Le 25/04/2016 16:41, Daniel Roe a écrit :
>>
>> 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 The documentation for 'volmap' is a bit out of date.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
>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
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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
(801) 585-6208 (Fax)
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Received on Mon Apr 25 2016 - 13:00:03 PDT
