Dear James,
I think your question is actually not suitable for the AMBER list.
Probably the most suitable is the VMD list. As I answered to you on the
NAMD list already, you can use the NetworkView as it is with Carma,
there is no need to generate a priori the matrix. You can use VMD to
create a PSF file (writepsf command) from any PDB file or AMBER
topology. Also you can use VMD (animate write dcd) to convert Amber
trajectories to dcd.
For sure you can also modify the NetworkView plugin to read in matrices
from other programs or to use other programs than carma to generate the
matrices, but you'd need to modify the tcl code of the plugin and unless
you are absolutely sure of what you are doing, I'd advise against this
option. Moreover, this option is significantly more work intense and
time consuming than my suggestion above.
Best wishes
Vlad
On 04/14/2015 08:32 PM, James Starlight wrote:
> Hi Dan and thanks for the ideas!
> Will it be possible to load cog-matrix calculated by cpp-traj directly
> to the NetworkView in vmd avoiding using of CARMA? BTW is it possible
> to convert parm7 to the pdf using some amber-tool?
>
> Thanks,
>
> James
>
> 2015-04-14 17:59 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
>> Hi,
>>
>> You can calculate various types of matrices with cpptraj ('matrix'
>> command). You can also diagonalize the matrix and optionally write out
>> nmwiz-compatible output ('diagmatrix' command). Cpptraj can use PSF
>> and DCD files as well. See the Amber 14 manual for more details.
>>
>> -Dan
>>
>> On Tue, Apr 14, 2015 at 8:25 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>> Dear Amber users!
>>>
>>> I wonder to ask whether someone used VMDs NetworkView plugin for the
>>> analysis of the biosimulations carried out in Amber? From the tutorial
>>> I've found that to calculate covariance matrix prior to Networks
>>> calculations some external programs like CARMA are used which directly
>>> works with the NAMD-like psf topologies. Are there any other
>>> possibilities to do the same using amber-like inputs?
>>>
>>>
>>> Thanks!
>>>
>>> James
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> --
>> -------------------------
>> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Apr 14 2015 - 12:30:02 PDT
