Hi, I've been developing an evolutionary algorithm which I would like to integrate it with Gromacs. Thus, in this moment, I'm updating my own code to attend the Gromacs patterns.
Based on charmm27.ff directory I've built h files which contain some amino acids (ALA, GLY and ARG). I'm modelling my algorithm I'll put more amino. However, if you want to see my files, please see the main in [1]. I create that file for mapping the files of charmm27.ff instead of work with .c files from pdb2gmx. Maybe if you create your charmm file mapping your job will be easier. [1] http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/topology_charmm27_parameters.h Thanks in advance, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Wed, Jul 21, 2010 at 1:38 PM, Sai Pooja <saipo...@gmail.com> wrote: > Thanks Rodrigo. I have read the paper and and I am familiar with the > topology folder. > This is what I want to do: > > I have a version of gromacs without the charmm forcefield which I have > modified to use an algorithm I need. > > However, I now need to use charmm ff with this algorithm and in gromacs. > > It would be extremely tedious to modify another version of gromacs(with > charmm ff i.e.) for this algorithm. So , I was thinking if I could just copy > the top folder from a git version of gromacs(with charmmff) and make changes > in configure files to make it work with my version? > > Can someone give me some pointers on this? For example which files much be > changed/ modified? > > I have some thoughts: > 1. Clearly, the topology folder has been changed. It has new files on > charmm and the organization of files has also been changed --> cp topology > folder from git and put into my version > > 2. Make changes in configure.ac > The git version have extra commands for compiling top files for each > forcefield - copy those commands exactly from the git version and add to my > version. > > 3. I think that some files connected to pdb2gmx might have to be changed. > Which ones I am not sure. I am only interested in the .c files. Maybe > toppush.c? > > What else would I need to change? Any pointers would be very helpful. > Kindly let me know even if you have attempted something similar. > > Thanks > Pooja > > On Tue, Jul 20, 2010 at 8:14 PM, Rodrigo Faccioli < > rodrigo_facci...@uol.com.br> wrote: > >> Hi, >> >> The gromacs version in git master, please see the directory >> share/top/charmm27.ff >> >> That directory contains whole gromacs charmm files. Furthermore, please >> see the reference below which explain more details about these parameters. >> >> Bjelkmar, Larsson, Cuendet, Hess, and Lindahl, JCTC 2010 >> >> I hope those informations help you. >> >> What do you want to do more specific? >> >> -- >> Rodrigo Antonio Faccioli >> Ph.D Student in Electrical Engineering >> University of Sao Paulo - USP >> Engineering School of Sao Carlos - EESC >> Department of Electrical Engineering - SEL >> Intelligent System in Structure Bioinformatics >> http://laips.sel.eesc.usp.br >> Phone: 55 (16) 3373-9366 Ext 229 >> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 >> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 >> >> >> On Tue, Jul 20, 2010 at 6:57 PM, Sai Pooja <saipo...@gmail.com> wrote: >> >>> Hi, >>> >>> If one has to make a version of gromacs charmm compatible, which files >>> from the charmm compatible version must be looked at? >>> >>> Pooja >>> >>> -- >>> Quaerendo Invenietis-Seek and you shall discover. >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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