On Mon, Feb 15, 2016 at 11:51 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> What is the file format *.nc and how can I use it and see its contents?
The '.nc' extension is associated with the Amber NetCDF trajectory
format in cpptraj, but the trajectory can be written in any format
cpptraj supports. For trajectory output in cpptraj, if no trajectory
format keyword is specified the format is auto-detected from the file
name extension. For a list of supported trajectory file formats and
their extensions please see table 29.3 in the Amber 15 manual, section
29.7 'Trajectory File Commands', page 540.
-Dan
>
> Regards,
> Michael
>
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il
>
> ________________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Monday, February 15, 2016 6:59 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] average 3D structure with condition
>
> Hi,
>
> On Mon, Feb 15, 2016 at 9:42 AM, Michael Shokhen
> <michael.shokhen.biu.ac.il> wrote:
>> center :1-508 mass origin
>> image origin center familiar
>> average av_md3-8.pdb PDB
>
> Note that you are only removing overall translational motion from your
> average structure via the 'center' command; rotational motion will
> still be present in the average. You may want to RMS best-fit to e.g.
> the first structure to remove this as well (unless you want rotational
> motion present for some reason). You also may want to try 'autoimage'
> instead of 'center'/'image'.
>
>> My question is: How to modify the cpptraj script in order to collect
>> for the averaging only that MD frames
>>
>> where the interatomic distance:
>>
>>
>> distance R5_E89 :5.67 :89.1503
>>
>> belongs to the interval from 3 to 5 A?
>
> You can use either the 'filter' command if you want to process only
> frames matching certain criteria with subsequent actions, or the
> 'outtraj' command with 'maxmin' keyword(s) if you only want to extract
> said frames. For example, if you only wanted to run the 'hbond'
> command on frames matching your specific criteria you could do
> something like:
>
> distance R5_E89 :5.67 :89.1503
> filter R5_E89 min 3 max 5
> hbond <hbond args>
>
> If you just want to extract frames with 'outtraj':
>
> distance R5_E89 :5.67 :89.1503
> outtraj Frames_R5_E89_3_5.nc maxmin R5_E89 min 3 max 5
>
> Hope this helps,
>
> -Dan
>
>>
>>
>> Many thanks,
>>
>> Michael
>>
>>
>>
>> *****************************
>> Michael Shokhen, PhD
>> Associate Professor
>> Department of Chemistry
>> Bar Ilan University,
>> Ramat Gan, 52900
>> Israel
>> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
>> _______________________________________________
>> 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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> 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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Received on Mon Feb 15 2016 - 13:30:03 PST
