e: [gmx-users] ambconv again
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
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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