Hi all. Firstly, thanks a lot for all the help! ;)
First, about reading the atom-names from a .gro file, I don't think it would "so painfull". It would "look like" a bit to having a well programmed "state machine" in the code. About the language, yes, I admit that bor reads and writes, fortran is miserable. But for calculations (like the inner codes of a certain program? ;) only joking... :D ) if one chooses not to go by assembly, fortran is still the way, specially if you consider the extra simplicity of fortran90. Anyway, I would not even consider re-writing the reads in fortran, but would love to consider to link to a library (like in reading .xtc files) or gromacs compiled object just to read it correctly. ;) About the box, is it on the .xtc file? Could not get the proper variable of it, could someone give me some infor which is that? Finally: yes, I considered changing everything to a .pdb file, despite the file size and the fact that I completelly forgot it could have the charges on it. But even so I would still have problems with the atomic masses, am I right? Or can I put that on a standard pdb file with gromacs programs? Again, tahnks a lot for all help in advance! Sincerally yours, Jones On 9/30/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > Mark Abraham wrote: > > Jones de Andrade wrote: > >> Hi Tsjerk. > >> > >> Thanks for the prompt answer. > >> > >> Good idea, I can take the atom names from a .gro file, nad, probably > >> some strange algorithm can also get the number of atoms per molecule > >> and number of molecules from there, am I right? That would help a lot. > > > > Simplest is to write a parser for a gmxdump of a .tpr file. This is what > > Perl was made for. If you're constrained to use Fortran for your > > analysis program, then developing an intermediate file format for it to > > parse might be worthwhile. > > > >> But: I'll still be unable to get atomic masses and point charges. No > >> to mention the box shape. :( And I'll need a way to read these > >> parameters too, unless I begin to write all them in a really awfull > >> and strange index file. > >> > >> From what I can understand on the "file logistics" of gromacs, these > >> information are only stored in the whole ".top .itp .atp .rtp > >> structure of files" or, in a condensed form, in the ".tpr" file. Is > >> that right? > > > > Yeah. Writing something to do the lookups in the .*tp files which grompp > > does to form the .tpr is asking for trouble. Do the lookup in the .tpr > > file. The .edr file has box dimensions, of course. > > > > All this makes it sound like you should be dropping Fortran and writing > > in C or Perl! > > > the box is in the xtc file, if you need the atom names a corresponding > pdb or gro file should do the trick. don't try to read tpr files or > gmxdumps of it, that's a complete waste of time. you can e.g. use > editconf to dump a pdb file with charges in the b-factor fields. > > And indeed, using fortran will make your life quite miserable for these > kind of things. > > -- > 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. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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