[gmx-users] Re: gmx-users Digest, Vol 47, Issue 41
sudheer babu
sudheer.pbm07 at gmail.com
Thu Mar 13 16:21:45 CET 2008
Thank you Mr.David.
On Thu, Mar 13, 2008 at 6:45 PM, <gmx-users-request at gromacs.org> wrote:
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Problem about *pdbgmx (sudheer babu)
> 2. Re: Problem about *pdbgmx (David van der Spoel)
> 3. Re: problem with mpi configuration. (Dr. Niharendu Choudhury)
> 4. Re: problem with mpi configuration. (Mark Abraham)
> 5. downloading problem (Siavoush Dastmalchi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Mar 2008 16:39:25 +0530
> From: "sudheer babu" <sudheer.pbm07 at gmail.com>
> Subject: [gmx-users] Problem about *pdbgmx
> To: gmx-users at gromacs.org
> Message-ID:
> <76de29310803130409m5ae36884v11356d43cfa8c408 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi gmx-users,
> I want to protonate only HIS residues in my protein , so I gave command
> like this *pdb2gmx -f protein.pdb -HIS then it asked which number of HIS
> to
> protonate, I gave numbers of HIS residues which I want protonate , it ran
> fine without error, but when I open conf.gro file, along with HISH, LYS
> also
> protonating and form LYSH. In input file LYS present like this. Why it
> happening like this?
> Pls help me.
> Thanks in advance.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/9258929c/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Thu, 13 Mar 2008 12:12:17 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Problem about *pdbgmx
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47D90C11.3010208 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> sudheer babu wrote:
> > Hi gmx-users,
> > I want to protonate only HIS residues in my protein , so I gave
> > command like this *pdb2gmx -f protein.pdb -HIS then it asked which
> > number of HIS to protonate, I gave numbers of HIS residues which I want
> > protonate , it ran fine without error, but when I open conf.gro file,
> > along with HISH, LYS also protonating and form LYSH. In input file LYS
> > present like this. Why it happening like this?
>
> that's default. use -lys flag and -arg and -glu and -asp
>
> > Pls help me.
> > Thanks in advance.
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 13 Mar 2008 16:57:45 +0530 (IST)
> From: "Dr. Niharendu Choudhury" <nihcho at barc.gov.in>
> Subject: Re: [gmx-users] problem with mpi configuration.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1205407665.47d90fb11caa7 at bts.barc.gov.in>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Pohl,
> I think your prefix directory /usr/local/gromacs332 is not accesible for
> writting. Try to creat new directories with other names and use those in
> prefix.
>
> Have you setenv for the include and lib of the fftw files?
>
> (For instance, assume we have installed FFTW with --prefix=/home/joe/fftw.
> If your shell is tcsh, you set
>
> setenv CPPFLAGS -I/home/joe/fftw/include
> setenv LDFLAGS -L/home/joe/fftw/lib
>
> or, if you are using a bash shell:
>
> export CPPFLAGS=-I/home/joe/fftw/include
> export LDFLAGS=-L/home/joe/fftw/lib )
>
> If not do that.
>
> Nihar
>
>
>
>
>
>
> Quoting Jens Pohl <Pohl.Jens at web.de>:
>
> >
> > > -----Ursprüngliche Nachricht-----
> > > Von: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > > Gesendet: 12.03.08 20:06:55
> > > An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > > Betreff: Re: [gmx-users] problem with mpi configuration.
> >
> >
> > > Thank you very much for help me.
> > > I have try to install gromacs 3.3.3 on rhel 4.0.
> > > I try to configure gromacs single with the command "./configure
> > --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but
> when I
> > try to install, I have this error:
> > > usr/bin/install: cannot create regular file
> > `/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No
> such
> > file or directory
> > > make[3]: *** [install-binPROGRAMS] Error 1
> > > make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
> > > make[2]: *** [install-am] Error 2
> > > make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
> > > make[1]: *** [install-recursive] Error 1
> > > make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'
> > > make: *** [install-recursive] Error 1
> > > I have try to edit the end of the configure command
> > "/usr/local/gromacs332" with"/usr/local/gromacs333" and
> "/usr/local/gromacs"
> > but
> > > I have anlogue errors. Can you help me?
> > >
> > > Thanks in advance.
> >
> > Hallo Mario!
> > (Maybe) you have to install as root. When I tried to install gromacs as
> user,
> > I had similar problems.
> > Jens
> >
> > >
> > > Mario
> > > Diego Enry <diego.enry at gmail.com> ha scritto: You should check the
> user
> > guide.
> > >
> > http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?
> s=docs<http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs>
> > >
> > > In a nutshell:
> > > 1) You need is to install mpich in all machines. Actually you can sync
> > > the mpich install directory (also gromacs).
> > > 2) You also need to have the same /etc/hosts on every machine. rsync
> that.
> > > 3) You need to grant ssh access without password by creating a rsa-key
> > > for every user
> > >
> > > Fell free to private message if you need any additional help.
> > >
> > > Ciao.
> > >
> > > On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy wrote:
> > > > Thank's Diego,
> > > > I'm grateful to you. I have only one question. How can I configure
> > mpi/lam
> > > > for
> > > relaize the comunication between nodes?
> > > > I have created an hostsfile with my ip addresses.
> > > > Thank's a lot in advance.
> > > >
> > > > Mario
> > > >
> > > > Diego Enry ha scritto:
> > > >
> > > > Since you didn't show us the problems you met.. try following this:
> > > >
> > > > #1) Download essential packages
> > > > #1.1) mpich
> > > > wget
> > > >
> >
> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-
> 1.0.6p1.tar.gz
> > > >
> > > > #1.2) fftw
> > > > wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz
> > > >
> > > > #1.3) gromacs
> > > > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz
> > > >
> > > >
> > > > #2) compile packages:
> > > >
> > > > #2.1) mpich
> > > > tar xvfz mpich2-1.0.6p1.tar.gz
> > > > cd mpich2-1.0.6p1
> > > > make distclean
> > > > ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
> > > > --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
> > > > make
> > > > make
> > > install
> > > > make distclean
> > > > cd ..
> > > >
> > > > #2.2) fftw single
> > > > tar xvfz fftw-3.1.2.tar.gz
> > > > cd fftw-3.1.2
> > > > make distclean
> > > > ./configure --enable-float --enable-sse --enable-threads
> > > > make
> > > > make install
> > > > make distclean
> > > > cd ..
> > > >
> > > > #2.3) gromacs single
> > > > tar xvfz gromacs-3.3.2.tar.gz
> > > > cd gromacs-3.3.2
> > > > ./configure --enable-mpi --program-suffix=_mpi
> > > > --prefix=/usr/local/gromacs332
> > > > make
> > > > make install
> > > > make links
> > > > make distclean
> > > > cd ..
> > > >
> > > > #2.4) fftw double
> > > > cd fftw-3.1.2
> > > > ./configure --enable-sse2 --enable-threads
> > > > make
> > > > make install
> > > > make distclean
> > > > cd ..
> > > >
> > > > #2.2) gromacs double
> > > > cd gromacs-3.3.2
> > > > ./configure --enable-mpi --program-suffix=_mpi_d
> > > > --prefix=/usr/local/gromacs332 --enable-double
> > > > make
> > > > make install
> > > > make
> > > links
> > > > make distclean
> > > > cd ..
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:
> > > > > Dear all,
> > > > > I'm tried to configure gromacs in parallel but I have meet some
> > problems.
> > > > > I don't understand if the problems are relative to mpi or gromacs
> > > > > configuration. For this reason I'd be grateful if you explained a
> > detailed
> > > > > installation procedure of all that require to run gromacs in
> parallel,
> > > > > started by mpi/lam configuration. I now that is an hard and
> demanding
> > > > > request, but it is a big help for me because you are only
> resource.
> > > > >
> > > > > Thank's in advance
> > > > >
> > > > > Mario
> > > > >
> > > > >
> > > > > ________________________________
> > > > > ________________________________
> > > > >
> > > > > L'email della prossima generazione? Puoi averla con la nuova
> Yahoo!
> > Mail
> > > > >
> > > _______________________________________________
> > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Diego Enry B. Gomes
> > > > Laboratório de Modelagem e Dinamica Molecular
> > > > Universidade Federal do Rio de Janeiro - Brasil.
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > > > Please don't post (un)subscribe requests to the list. Use
> > > the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > ________________________________
> > > > L'email della prossima generazione? Puoi averla con la nuova Yahoo!
> Mail
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > >
> > >
> > >
> > >
> > > --
> > > Diego Enry B. Gomes
> > > Laboratório de Modelagem e Dinamica Molecular
> > > Universidade Federal do Rio de Janeiro -
> > > Brasil.
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > >
> > >
> > >
> > >
> > > -----------------------------------------------------------------
> > > Inviato da Yahoo! Mail.
> > >
> > > Il servizio di posta con lo spazio illimitato.
> > >
> > > -----------------------------------------------------------------
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> posting!
> > > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >
> > _______________________________________________________________________
> > Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage
> > kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> *************************************************************************
> * *
> * Dr. Niharendu Choudhury Tel: 91-22-2559 5089 *
> * Theoretical Chemistry Section, Fax: 91-22-2550 5151 *
> * RC & CD Division, Chemistry Group, 91-22-2551-9613 *
> * Mod. Lab, Email: nihcho at barc.gov.in *
> * Trombay, Mumbai-400 085 *
> * INDIA *
> * *
> * Residence Tel. No. 91-22-2552 7832 *
> *************************************************************************
>
>
> -------------------------------------------------
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 13 Mar 2008 23:51:47 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] problem with mpi configuration.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47D92363.8040307 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dr. Niharendu Choudhury wrote:
> > Dear Pohl,
> > I think your prefix directory /usr/local/gromacs332 is not accesible for
> > writting. Try to creat new directories with other names and use those in
> > prefix.
>
> First, they need to fix their typo in their configure command line, as
> mentioned by another poster. Otherwise, it isn't known that the failure
> to write these files is caused by permission issues, rather than their
> malformed filename.
>
> > Have you setenv for the include and lib of the fftw files?
> >
> > (For instance, assume we have installed FFTW with
> --prefix=/home/joe/fftw.
> > If your shell is tcsh, you set
> >
> > setenv CPPFLAGS -I/home/joe/fftw/include
> > setenv LDFLAGS -L/home/joe/fftw/lib
> >
> > or, if you are using a bash shell:
> >
> > export CPPFLAGS=-I/home/joe/fftw/include
> > export LDFLAGS=-L/home/joe/fftw/lib )
> >
> > If not do that.
>
> This works, but it's superior to leave the environment alone and instead
> to use "./configure CPPFLAGS=-I/home/joe/fftw/include
> LDFLAGS=-L/home/joe/fftw/lib". Not only do you avoid having to get it
> right for each shell, but you don't pollute your environment for this
> shell (small point), and (more importantly) in config.log you will have
> a record of the command line for any subsequent time you need to run
> configure. When someone has to come back in 6 months to configure an MPI
> or double-precision version, the record of what was done last time saves
> on repeated detective work.
>
> If you need multiple -I or -L flags, then enclosing them in quotes,
> separated by spaces, works, i.e. "./configure LDFLAGS='-L/some/lib
> -L/some/other/lib'"
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 13 Mar 2008 16:44:14 +0330
> From: "Siavoush Dastmalchi" <Dastmalchi.s at tbzmed.ac.ir>
> Subject: [gmx-users] downloading problem
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <C8C110ABF258864B8AD00D320942B6273AE834 at exch-srv.tbzmed.ac.ir>
> Content-Type: text/plain; charset="windows-1256"
>
> Hi there,
>
> This may not be relevant to this list but I am hopping to get an answer.
> The problem is that I can't download the source code for Grommacs from the
> download site and it seems that the link to web interface to the ftp server
> is not working as well.
>
> I tried to use an ftp program to connect to ftp.gromacs.org but wasn't
> sure what should I use for User Name and Password.
>
> Many thanks in advance.
>
> Siavoush
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: not available
> Type: application/ms-tnef
> Size: 3100 bytes
> Desc: not available
> Url :
> http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/3b7e67b8/attachment.bin
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 47, Issue 41
> *****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080313/592eaa46/attachment.html>
More information about the gromacs.org_gmx-users
mailing list