<div><STRONG><EM>Alan <alanwilter@gmail.com></EM></STRONG> wrote: </div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"> <div>Hi Bruce, many thanks for your archive. Incidentally, I do use Mac!<BR>and I have quitted trying to adjust Makefile for ambconv to compile on<BR>Mac tiger intel.<BR><BR>Although your ambconv compiles here, it is still not working (giving<BR>"Bus error").<BR><BR>But then you mentioned you did "topolbuild". So I fetched for it and<BR>tried both in Mac tiger intel and Linux intel Ubuntu (with -lm).<BR>In mac topolbuild fails with "Bus error" and in Linux it fails with<BR>"segmentation fault". Antechamber 1.27 works fine here.<BR><BR>I hope I can solve this problems, but I must mention that your<BR>topolbuild approach is a very good inspiration since I want to do<BR>something similar from antechamber to generate CNS files with both<BR>topologies PROSLQ and OPLS.</div></BLOCKQUOTE> <div>I have
never tried these on an Intel based system at all. Neither program corrects</div> <div>for differences in endianness between Intel and powerpc (or Sparc or Mips as well</div> <div>both of which have the same endianness as powerpc) that might cause problems.</div> <div>I have been trying to correct for my lack of access to Intel based systems to see</div> <div>what problems might arise with them, but without much success so far. What you</div> <div>are experiencing might also be a compiler problem. I know that compilation with</div> <div>gcc 3.3 produces code that works and compilation with at least one out of the gcc</div> <div>4 series does not. Probably this is the same problem that affects gromacs compilation</div> <div>with at least one out of the gcc 4 series.</div> <div> </div> <div>With respect to the version of ambconv I attached, just like the original ambconv, it</div> <div>requires the old format of leap
output rather than the new. I did not have time to make</div> <div>the vast number of input corrections that would have been required to make it take the</div> <div>new format. Indeed, my opinion of ambconv was that it has so many problems in the</div> <div>code that it would benefit greatly from an absolutely thorough rewrite. I did, however,</div> <div>correct the input so that it does not require one to edit one of the initial lines of the</div> <div>leap output before using ambconv. However, the consequence of that correction is that</div> <div>it will suffer a bus error if that line is edited as was required by the original ambconv.</div> <div> </div> <div>As for topolbuild, I have a personal version that does produce from Sybyl mol2 input</div> <div>the skeletons for CNS param, and top files, and a pdb file. However, I do not have</div> <div>appropriately laid out parameter tables to correctly fill in
the forcefield parameters with</div> <div>values appropriate for use within CNS. Thus, I have had to severly edit the results after</div> <div>running topolbuild. In addition, OPLS or PROLSQ atom type translation tables,</div> <div>although addition of the ability to use these would not be difficult. Indeed, the current</div> <div>iteration of topolbuild on which I am still working would make such additions easier.</div> <div> </div> <div> </div> <div>Sincerely,</div> <div> </div> <div> </div> <div>-- </div> <div>Bruce D. Ray, Ph.D.</div> <div>Associate Scientist, and Operations Director</div> <div>NMRCenter </div> <div>IUPUI Physics Dept.</div> <div>402 N. Blackford St.</div> <div>Indianapolis, IN 46202-3273</div><BR><BR><p> 
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