Hi all.<br><br>Firstly, thanks a lot for all the help! ;)<br><br>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.
<br><br>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. ;)
<br><br>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?<br><br>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?
<br><br>Again, tahnks a lot for all help in advance!<br><br>Sincerally yours,<br><br>Jones<br><br><div><span class="gmail_quote">On 9/30/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Mark Abraham wrote:<br>> Jones de Andrade wrote:
<br>>> Hi Tsjerk.<br>>><br>>> Thanks for the prompt answer.<br>>><br>>> Good idea, I can take the atom names from a .gro file, nad, probably<br>>> some strange algorithm can also get the number of atoms per molecule
<br>>> and number of molecules from there, am I right? That would help a lot.<br>><br>> Simplest is to write a parser for a gmxdump of a .tpr file. This is what<br>> Perl was made for. If you're constrained to use Fortran for your
<br>> analysis program, then developing an intermediate file format for it to<br>> parse might be worthwhile.<br>><br>>> But: I'll still be unable to get atomic masses and point charges. No<br>>> to mention the box shape. :( And I'll need a way to read these
<br>>> parameters too, unless I begin to write all them in a really awfull<br>>> and strange index file.<br>>><br>>> From what I can understand on the "file logistics" of gromacs, these<br>
>> information are only stored in the whole ".top .itp .atp .rtp<br>>> structure of files" or, in a condensed form, in the ".tpr" file. Is<br>>> that right?<br>><br>> Yeah. Writing something to do the lookups in the .*tp files which grompp
<br>> does to form the .tpr is asking for trouble. Do the lookup in the .tpr<br>> file. The .edr file has box dimensions, of course.<br>><br>> All this makes it sound like you should be dropping Fortran and writing
<br>> in C or Perl!<br>><br>the box is in the xtc file, if you need the atom names a corresponding<br>pdb or gro file should do the trick. don't try to read tpr files or<br>gmxdumps of it, that's a complete waste of time. you can
e.g. use<br>editconf to dump a pdb file with charges in the b-factor fields.<br><br>And indeed, using fortran will make your life quite miserable for these<br>kind of things.<br><br>--<br>David van der Spoel, Ph.D.<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">
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