then what is the force field that suitable for my work? Regard,
On Thu, Jul 22, 2010 at 11:58 PM, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[email protected]> > Subject: Re: [gmx-users] The grompp problem!! (Urgently) > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > 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 <[email protected]> > > > 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, > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.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 [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100722/966859be/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 22 Jul 2010 12:51:53 +0200 > From: Florian Dommert <[email protected]> > Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Skipped content of type multipart/alternative-------------- next part > -------------- > A non-text attachment was scrubbed... > Name: signature.asc > Type: application/pgp-signature > Size: 259 bytes > Desc: OpenPGP digital signature > Url : > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100722/be084e87/signature-0001.bin > > ------------------------------ > > Message: 3 > Date: Thu, 22 Jul 2010 11:02:17 -0400 > From: Sai Pooja <[email protected]> > Subject: [gmx-users] Backward compatibility of charmm-ff > implementation > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > 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. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100722/df3b607e/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 22 Jul 2010 18:58:10 +0200 > From: KACHMAR Ali <[email protected]> > Subject: RE: [gmx-users] installation: gromacs on Mac.10.5.8 leopard > To: <[email protected]> > Message-ID: <[email protected]> > 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: [email protected] > To: [email protected] > 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: [email protected] > > > > > To: [email protected] > > > > > 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 [email protected] > > > > > http://lists.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 > [email protected]. > > > > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > De nouvelles Emoticones sur Messenger ? Téléchargez > gratuitement les émoticônes Summer ! > > > > > > -- > > > Ansgar Esztermann > > > DV-Systemadministration > > > Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 > > > > > > -- > > > gmx-users mailing list [email protected] > > > http://lists.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 [email protected]. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > Le nouveau Messenger arrive ! Téléchargez-le > gratuitement et découvrez ses nouvelles fonctionnalités > > > > > -- > Florian Dommert > Dipl. Phys. > > Institute for Computational Physics > University Stuttgart > > Pfaffenwaldring 27 > 70565 Stuttgart > > Germany > > Tel: +49 - 711 / 6856-3613 > Fax: +49 - 711 / 6856-3658 > > EMail: [email protected] > Home: > http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert<http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert> > > !! 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