That is not about any kind of etiquette. Despite enormous efforts of those developers the package is barely usefull, that is it.<br><br><b><i>Daan van Aalten <vdava@davapc1.bioch.dundee.ac.uk></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> <br>Dear Daniela<br><br>Sorry, but I have to agree with Mark Abraham here.<br><br>Although I haven't done much useful development myself apart from perhaps<br>PRODRG, the tone of some of the questions asked absolutely amazes me.<br>There seems to be no respect for the huge amount of work developers put<br>into a package like Gromacs - new people come in and "just expect it to<br>work" and if it doesn't then of course it's not their fault but that of<br>the developers. Gromacs is *free* and the developers have no formal<br>obligation whatsoever to help you in any way. I am sure everyone<br>involved with Gromacs is keen to continually improve the code and
would<br>like to here about problems/bugs etc - but in properly worded E-mails,<br>giving constructive feedback, not some kind of shouting match.<br><br>I normally think that E-mails like that of Yegor Isakov don't even deserve<br>a response, but yours does as it is an important point of dicussion.<br><br>Daan<br><br><br>On Thu, 23 Feb 2006, Daniela S. Mueller wrote:<br><br>> hi,<br>><br>> On Thu, 2006-02-23 at 12:42 +1100, Mark Abraham wrote:<br>> > Yegor Isakov wrote:<br>> ><br>> > You are much more likely to get a helpful response from the people who<br>> > know this software best (the programmers, who do read this list) if you<br>> > express a little less of your frustration, and imply less condemnation<br>> > of their software design choices, which you probably don't understand<br>> > yet anyway!<br>> ><br>><br>> though it might be unpleasant or even unjustified, frustrated reactions<br>> like these are in a way
understandable.<br>><br>> what i find less understandable and certainly a great deal less<br>> tolerable, is the arrogance and judgement of some users of this list<br>> towards others.<br>><br>> also it would make helpful responses much likelier, if those unhelpful<br>> responses were omitted.<br>><br>> regards,<br>> daniela<br>><br>><br>> > Check your assumptions - you haven't paid anybody for the right to rant<br>> > at them :-) You'd also do well to remember that GROMACS doesn't come<br>> > with a warranty of fitness for any purpose :-)<br>> ><br>> > > I would be extremely pleased if anybody would tell me how could I foce<br>> > > that stupid pdb2gmx program to follow the path to the directory<br>> > > containing .itp files (~/share/top).<br>> ><br>> > Setting the environment variable GMXLIB makes various GROMACS utilities<br>> > look there instead of the default, which is
probably<br>> > $GMXDATA/gromacs/top. GMXDATA gets set when you run GMXRC which is<br>> > installed in the same place as the GROMACS binaries. You may need to<br>> > link the existing contents of $GMXDATA/gromacs/top/ to ~/share/top/ in<br>> > order to have everything work, as I couldn't get GMXLIB to accept a path.<br>> ><br>> > I note that the manual mentions GMXLIB only in passing in a few of the<br>> > programs' man pages, and not at all in the Appendix section on<br>> > Environment variables. Usage of GMXRC is also not mentioned in the<br>> > installation section on the web page. Can either of both of these be<br>> > looked at, please?<br>> ><br>> > > Although in the manual it was recomended to avoid modifying .rtp files,<br>> > > that is the only way I found to produce a topology "semi-automatically."<br>> > > Is there any other reasonable way to produce a topology? Is
anywhere<br>> > > more intelegent converter of pdb files? Is anywhere a program that<br>> > > permits creating a stable bond between 2 atoms in a topolgy without<br>> > > blowing up the last one?<br>> ><br>> > Construction of topologies for MM calculations is a process that<br>> > involves making judgements. Automating "sensible" defaults is an<br>> > extremely tricky business, given the multiplicity of force fields, the<br>> > kinds of kludgey PDB files that you can get hit with, and the<br>> > innumerability of the molecules people will want to use. Then of course,<br>> > a default someone thinks is sensible, someone else will think is<br>> > ludicrous, and they might both be right for different applications.<br>> > Basically you will need to do some work yourself if you are doing<br>> > something new... big surprise.<br>> ><br>> > Mark<br>><br>><br>> --<br>><br>>
Daniela S. Mueller<br>><br>> biologist (Diplom, German degree)<br>> ______________________________________________________________________<br>><br>> - Molecular Dynamics Group, UQ -<br>><br>> Address:<br>> School of Molecular and Microbial Sciences (SMMS)<br>> Chemistry Building (#68)<br>> University of Queensland<br>> Qld 4072, Brisbane<br>> Australia<br>><br>> Phone: +61-7-33653732<br>><br>> Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm<br>><br>> **********************************************************************<br>><br>> - MD group, RuG -<br>><br>> Address:<br>> Molecular Dynamics<br>> Dept. of Biophysical Chemistry<br>> University of Groningen<br>> Nijenborgh 4<br>> 9747 AG Groningen<br>> The Netherlands<br>><br>> Website: http://www.rug.nl/gbb/md<br>> ______________________________________________________________________<br>><br>>
_______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>><br><br><br>##############################################################################<br>Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader<br>Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979<br>Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764<br>School of Life Sciences E-mail: see WWW page<br>Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't
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