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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Received on Mon Apr 25 2016 - 06:30:04 PDT
