Alan <[EMAIL PROTECTED]> 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.
Sincerely,
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMRCenter
IUPUI Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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