Dear Dan
Is there a way to convert CpptrajPairDist into text file or is there any
utilities which can automatically convert into text file?
Thanks
On Sat, Dec 28, 2013 at 2:58 PM, JAIME RUBIO MARTINEZ <jaime.rubio.ub.edu>
wrote:
> 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
> >>
> >>
> >>
> >>
> >> Aquest correu electrònic i els annexos poden contenir informació
> >> confidencial o protegida legalment i està adreçat exclusivament a la
> >> persona o entitat destinatària. Si no sou el destinatari final o la
> persona
> >> encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo,
> >> modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si
> heu
> >> rebut aquest correu electrònic per error, us preguem que n’informeu al
> >> remitent i que elimineu del sistema el missatge i el material annex que
> >> pugui contenir. Gràcies per la vostra col·laboració.
> >>
> >> 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.
> >> _______________________________________________
> >> 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 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> Aquest correu electrònic i els annexos poden contenir informació
> confidencial o protegida legalment i està adreçat exclusivament a la
> persona o entitat destinatària. Si no sou el destinatari final o la persona
> encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo,
> modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu
> rebut aquest correu electrònic per error, us preguem que n’informeu al
> remitent i que elimineu del sistema el missatge i el material annex que
> pugui contenir. Gràcies per la vostra col·laboració.
>
> 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.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
regards
Bharat Lakhani
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 21 2015 - 20:00:02 PDT
