Thanks so much!
A+,
James
2015-04-14 21:19 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>:
> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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)
>>>>
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
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>>>
>>>
>>
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Received on Wed Apr 15 2015 - 06:00:07 PDT
