Just to make it more clear, the PSF you generate with the writepsf
command in VMD from a PDB file or an AMBER topology will not be a PSF
with all the correct force field information. However, as the
NetworkView plugin only needs it to generate a covariance matrix from
the trajectory it does not require the force field info besides the atom
names and numbers to match to the trajectory file.
Best
Vlad
On 04/14/2015 09:11 PM, Vlad Cojocaru wrote:
> 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
>>>>
>>>> _______________________________________________
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>>>> 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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>> AMBER.ambermd.org
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>>
>>
>
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Received on Tue Apr 14 2015 - 12:30:03 PDT
