[gmx-users] Re: gmx-users Digest, Vol 75, Issue 117

Fri Jul 23 06:06:32 CEST 2010

then what is the force field that suitable for my work?

Regard,

On Thu, Jul 22, 2010 at 11:58 PM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
>
>   1. Re: The grompp problem!! (Urgently) (Krzysztof Mlynarczyk)
>   2. Re: installation: gromacs on Mac.10.5.8 leopard (Florian Dommert)
>   3. Backward compatibility of charmm-ff implementation (Sai Pooja)
>   4. RE: installation: gromacs on Mac.10.5.8 leopard (KACHMAR Ali)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 22 Jul 2010 12:24:16 +0200
> From: Krzysztof Mlynarczyk <mitomaster at gmail.com>
> Subject: Re: [gmx-users] The grompp problem!! (Urgently)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <AANLkTinx7=iS-YuwnEO=mCkuMco0htMPfP2JBhRLWOnr at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> If this is the tutorial I have in front of my eyes, then the problem is
> that
> order of force fields changed and "gromacs force field" you are told to
> choose is no longer under "0" as it is deprecated. "0" is ffG43a1, where
> this atom type is not present anymore.
>
> Good luck,
> Chris
>
> 2010/7/22 Yuranat Saikatikorn <sugazy at gmail.com>
>
> > I am doing the Drug-enzyme tutorial.
> > I also generated the drg.itp, drg.gro files using PRODRG server.
> > However, when I use the grompp command before the energy minimization
> > I face some error
> >
> >       >A fatal error was shown: atom types CR61 not found
> >
> > The atom type CR61 is presented in the drg.itp file that I included to
> .top file before using grompp.
> >
> > What should I do to get through this error?
> >
> > Many thanks
> >
> > Yuranat,
> >
> >
> > --
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> Message: 2
> Date: Thu, 22 Jul 2010 12:51:53 +0200
> From: Florian Dommert <dommert at icp.uni-stuttgart.de>
> Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4C4822C9.30208 at icp.uni-stuttgart.de>
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> ------------------------------
>
> Message: 3
> Date: Thu, 22 Jul 2010 11:02:17 -0400
> From: Sai Pooja <saipooja at gmail.com>
> Subject: [gmx-users] Backward compatibility of charmm-ff
>        implementation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <AANLkTimIsGoIgPO2PKbDYZYB5xjWtQRjFOqMWdePmQmN at mail.gmail.com>
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>
> Hi,
>
> I used the git version of gromacs_with_charmm27_forcefield_nocmap(June, 20,
> 2010) to generate .gro and .top files. I then used these files on
> gromacs-4.07 by copying the charmm27-ff library to my working directory.
> Since I was not using cmap, gb and nucleic acid and lipids I deleted those
> files in the charmm-ff library.
>
> I am able to use these files(.gro and .top) on gromacs-4.07 with grompp to
> generate .tpr files. Could this lead to errors I cannot foresee?
>
> Regards
> Pooja
>
>
> --
> Quaerendo Invenietis-Seek and you shall discover.
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> ------------------------------
>
> Message: 4
> Date: Thu, 22 Jul 2010 18:58:10 +0200
> From: KACHMAR Ali <kachmar_ali at hotmail.fr>
> Subject: RE: [gmx-users] installation: gromacs on Mac.10.5.8 leopard
> To: <gmx-users at gromacs.org>
> Message-ID: <COL115-W5640CFD9ECABA194E433B0FEA20 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi Florian,
> Thanks for your answer. You're right, I found I don't have lam in my
> usr/local/. Where I should download this package?
> It is not coming on the developer. What I install, it is just this OpenMPI
> The latest OpenMPI source from
> http://www.open-mpi.org/software/ompi/v1.2/downloads/openmpi-1.2.8.tar.bz2
>
> Could you please give the link for this OpenMPI/LAM.
> As you advised me I disable this command export
> CPPFLAGS=-I/usr/local/openmpi/include, and I tried again, still the same
> error.
> Thanks.
> AliDate: Thu, 22 Jul 2010 12:51:53 +0200
> From: dommert at icp.uni-stuttgart.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard
>
>
>
>
>
>
>
>
>
> Hello Ali,
>
>
>
>  starting with OS X 10.5 the Developer tools included also a nicely
> working distribution of OpenMPI. So as soon as the Developer Tools have
> been installed on the Mac following the steps on the GROMACS website
> allowed to compile parallel binaries. Taking a look at your
> bash_profile open several questions. Have you installed a self compiled
> version of OpenMPI and LAM, because you define corresponding
> environment variables ? It is also somehow uncommon that you find
> binaries in a directory usually dedicated for libraries like
> /usr/local/lib.
>
>
>
> On 22.07.10 11:00, KACHMAR Ali wrote:
>
>  > > export PATH=$PATH:/usr/local/lib
>
> > > export PATH=$PATH: /usr/bin/mpicc
>
> > > export PATH=$PATH:/usr/local/lam/bin/
>
> > >
>
>
>
> In this three lines it seems you try to define the compilers, but take
> a look at your environment variable PATH. Somewhere at the beginning
> you should find the directory /usr/bin as set by the system wide
> bash_profile. So the configure scripts usually chooses  the compilers
> contained in this directory. In your case it will be the gcc and mpicc
> compilers and linkers supplied by the Developer tools.
>
>
>  > >
>
> > > export CPPFLAGS=-I/usr/local/openmpi/include
>
> > >
>
>
>
>
>
> Why do you involve now this header files, perhaps they do not suit to
> the used version of OpenMPI ?
>
>
>
> Disable this lines in your .bash_profile open a new terminal and try
> again, perhaps this solves the problem. Then we know that just the path
> of the different installed MPI distributions were messed up.
>
>
>
> Cheers,
>
>
>
> Flo
>
>
>
> > > PS: the gcc is under the directory: /usr/local/lib or
> /usr/lib.
>
>
>  > >
>
> > > Thanks.
>
> > >
>
> > > Ali
>
> > >
>
> > >
>
> > >
>
> > > > From: Ansgar.Esztermann at mpi-bpc.mpg.de
>
> > > > To: gmx-users at gromacs.org
>
> > > > Date: Wed, 21 Jul 2010 12:15:25 +0200
>
> > > > Subject: Re: [gmx-users] installation: gromacs on
> Mac.10.5.8 leopard
>
> > > >
>
> > > >
>
> > > > On Jul 21, 2010, at 11:07 , KACHMAR Ali wrote:
>
> > > >
>
> > > > > checking whether the MPI cc command works...
> configure: error: Cannot compile and link MPI code with mpicc
>
> > > >
>
> > > >
>
> > > > This is the immediate problem: something goes wrong when
> compiling a test program with mpicc. If you look into the configure
> log, you should find a more detailed explanation of what went wrong
> (somewhere near the end).
>
> > > >
>
> > > > Regards,
>
> > > >
>
> > > > A.
>
> > > > --
>
> > > > Ansgar Esztermann
>
> > > > DV-Systemadministration
>
> > > > Max-Planck-Institut für biophysikalische Chemie,
> Abteilung 105
>
> > > >
>
> > > > --
>
> > > > gmx-users mailing list gmx-users at gromacs.org
>
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>
> > --
>
> > Ansgar Esztermann
>
> > DV-Systemadministration
>
> > Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
>
> >
>
> > --
>
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> --
> Florian Dommert
> Dipl. Phys.
>
> Institute for Computational Physics
> University Stuttgart
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>
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>
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>
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