Thanks,
I think 2srms is the best option for my goal.
Jaime
________________________________________
De: Daniel Roe [daniel.r.roe.gmail.com]
Enviado: martes, 17 de diciembre de 2013 22:52
Para: AMBER Mailing List
Asunto: Re: [AMBER] CpptrajPairDist
Of course, if all you need is the raw 2D RMSD matrix, you can also get it
directly from the rms2d/2drms command in cpptraj, which has some more
formatting options (such as gnuplot output etc).
-Dan
On Tue, Dec 17, 2013 at 2:44 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The CpptrajPairDist file is binary; the exact format depends on what
> version of cpptraj generated the file (since earlier versions had no
> concept of 'sieve'). The CpptrajPairDist file starts with a 4 byte header
> containing the characters 'C' 'T' 'M' followed by the version number. A
> quick way to figure out the version is to use the linux 'od' command to
> output the first 4 bytes as hexadecimal, e.g.:
>
> $ od -t x1 -N 4 CpptrajPairDist
> 0000000 43 54 4d 02
>
> So the CpptrajPairDist file version in the above example is 2.
>
> The next few numbers describe the matrix size and depend on the version.
>
> Version 0: Two 4-byte integers: # of rows and # of elements.
> Version 1: Two 8-byte unsigned integers (equivalent to size_t on most
> systems): # of rows and # of elements.
> Version 2: Three 8 byte unsigned integers: original # of rows, actual # of
> rows, and sieve value.
>
> This is followed by the actual matrix data, stored as a single array of
> floats (4 bytes). For versions 1 and 2 the number of elements is explicitly
> stored. For version 2, to calculate the number of matrix elements you need
> to read:
>
> Elements = (actual_rows * (actual_rows - 1)) / 2
>
> The cluster pair-distance matrix is an upper-right triangle matrix without
> the diagonal (in row-major order), so the first element is the distance
> between elements 0 and 1, the second is between elements 0 and 2, etc.
>
> In version 2 files, if the sieve value is greater than 1 that means
> original_rows > actual_rows and there is an additional array of characters
> original_nrows long, with 'T' if the row is being ignored (i.e. it was
> sieved out) and 'F' if the row is active (i.e. is active in the actual
> pairwise-distance matrix).
>
> The code that cpptraj uses to read in CpptrajPairDist files is in
> ClusterMatrix::LoadFile() (ClusterMatrix.cpp). Let me know if you have more
> questions.
>
> -Dan
>
>
>
> On Tue, Dec 17, 2013 at 12:37 PM, JAIME RUBIO MARTINEZ <jaime.rubio.ub.edu
> > wrote:
>
>>
>> I want to use the CpptrajPairDist file from the cluster savepairdist
>> command of cpptraj
>> to analyse the RMSD distance matrix, but I do not know how to extract the
>> data.
>>
>> can anyone give me info on the format of this file?
>>
>> Thanks
>>
>> Jaime
>>
>>
>>
>>
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Este correo electrónico y sus anexos pueden contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no es el destinatario final o la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha recibido este mensaje electrónico por error, le rogamos que informe al remitente y elimine del sistema el mensaje y el material anexo que pueda contener. Gracias por su colaboración.
This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration.
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Received on Sat Dec 28 2013 - 12:00:02 PST
