e: [gmx-users] ambconv again

Bruce Ray brucedray at yahoo.com
Sun Mar 16 22:23:50 CET 2008

Alan <alanwilter at gmail.com> wrote: 
    Hi Bruce, many thanks for your archive. Incidentally, I do use Mac!
and I have quitted trying to adjust Makefile for ambconv to compile on
Mac tiger intel.

Although your ambconv compiles here, it is still not working (giving
"Bus error").

But then you mentioned you did "topolbuild". So I fetched for it and
tried both in Mac tiger intel and Linux intel Ubuntu (with -lm).
In mac topolbuild fails with "Bus error" and in Linux it fails with
"segmentation fault". Antechamber 1.27 works fine here.

I hope I can solve this problems, but I must mention that your
topolbuild approach is a very good inspiration since I want to do
something similar from antechamber to generate CNS files with both
topologies PROSLQ and OPLS.
  I have never tried these on an Intel based system at all.  Neither program corrects
  for differences in endianness between Intel and powerpc (or Sparc or Mips as well
  both of which have the same endianness as powerpc) that might cause problems.
  I have been trying to correct for my lack of access to Intel based systems to see
  what problems might arise with them, but without much success so far.  What you
  are experiencing might also be a compiler problem.  I know that compilation with
  gcc 3.3 produces code that works and compilation with at least one out of the gcc
  4 series does not.  Probably this is the same problem that affects gromacs compilation
  with at least one out of the gcc 4 series.
  With respect to the version of ambconv I attached, just like the original ambconv, it
  requires the old format of leap output rather than the new.  I did not have time to make
  the vast number of input corrections that would have been required to make it take the
  new format.  Indeed, my opinion of ambconv was that it has so many problems in the
  code that it would benefit greatly from an absolutely thorough rewrite.  I did, however,
  correct the input so that it does not require one to edit one of the initial lines of the
  leap output before using ambconv.  However, the consequence of that correction is that
  it will suffer a bus error if that line is edited as was required by the original ambconv.
  As for topolbuild, I have a personal version that does produce from Sybyl mol2 input
  the skeletons for CNS param, and top files, and a pdb file.  However, I do not have
  appropriately laid out parameter tables to correctly fill in the forcefield parameters with
  values appropriate for use within CNS.  Thus, I have had to severly edit the results after
  running topolbuild.  In addition, OPLS or PROLSQ atom type translation tables,
  although addition of the ability to use these would not be difficult.  Indeed, the current
  iteration of topolbuild on which I am still working would make such additions easier.
  Bruce D. Ray, Ph.D.
  Associate Scientist, and Operations Director
  IUPUI Physics Dept.
  402 N. Blackford St.
  Indianapolis, IN 46202-3273

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