Re: extracting waters from DCD

From: yi wang (yiwang_at_ks.uiuc.edu)
Date: Wed Aug 09 2006 - 10:38:00 CDT

HI Neela,
      Here is the link to the matdcd script
http://www.ks.uiuc.edu/Development/MDTools/matdcd/
      There are actually some other useful tools along with matdcd at
http://www.ks.uiuc.edu/Development/MDTools/
Enjoy!
yi
On Aug 8, 2006, at 5:24 PM, Neelanjana Sengupta wrote:

> Hi Yi,
> This sounds like a blessing! Usually, when I have to do time intensive
> calculations with the atom coordinates, I save them in text format
> using tcl, and then write C++ codes.
> Could to tell me how/where to get this matlab code that can directly
> read the binary dcd files?
> Thanks!!
> -Neela
>
> On 8/8/06, yi wang <yiwang_at_ks.uiuc.edu> wrote:
>> > write a dcd file with changing atom numbers, which is very likely
>> the
>> > case if you select only those atoms within certain distance of the
>> > protein. But if you'd like to perform analysis on the coordinates,
>> > Justin has a script called 'matdcd' which allows you to input the
>> dcd
>> > files into matlab and manipulate it there, which is very fast.
>> >
>> > On Aug 8, 2006, at 3:55 PM, Jerome Henin wrote:
>> >
>> >> Dear Nar,
>> >> The DCD format imposes that all frames have the same number of
>> atoms.
>> >> So the
>> >> only way I see would be to have a VMD script that does the
>> selection,
>> >> updates
>> >> it for each frame and saves coordinates to separate per-frame
>> files.
>> >> Binary
>> >> files (like namdbin) would use much less disk space than PDB or
>> >> similar
>> >> text-based formats.
>> >> Jerome
>> >>
>> >> On Tuesday 08 August 2006 15:04, Narender Singh Maan wrote:
>> >>> Dear All,
>> >>> I have a trajectory file for my simulation of a protein in a big
>> >>> water box.
>> >>> Now to reduce the size i can extract and writeout the trajectory
>> for
>> >>> 'just
>> >>> the protein' from this system by using "catdcd" but my aim is to
>> >>> extract
>> >>> some waters also (only those water molecules which are within 3.5
>> >>> Ang. of
>> >>> the protein surface...for each frame).Any suggestions would be of
>> >>> great
>> >>> help.
>> >>> thanks
>> >>> Nar
>> >>>
>> > Thanks!
>> >
>> > yi =]
>> >
>> >
>> Thanks!
>>
>> yi =]
>>
>>
Thanks!

yi =]

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