Dear Madam or Sir,
When I used Openbabel to convert a fasta file into PDB format, I met a problem.
My fasta file is like
>protein
A
It is a protein, but the retrieved PDB was DNA structure.
How could I restrain the input parameters to output a protein structure?
Thank you very much!!
your sinc
Hi list,
In the ChangeLog I found Tim wrote about the GCC compilation options to
be used in order to enable MMFF94 parallelization. His entry reads as
follows.
2008-04-28 Tim Vandermeersch
* src/forcefields/forcefieldmmff94.cpp: OpenMP version of MMFF94. Does
not affect norma
Hi list,
In a previous version of OpenBabel (OpenBabel-2.2) it was possible to
instruct the build to make use of OpenMP to parallelize the forcefields
routines in OpenBabel. The way it was done was using compiler flags read
by the configure command inside babel source directory:
$tar zxvf ope
> This is from the time before OpenBabel moved to CMake. I look at the
> CMakeLists.txt and there is no OpenMP flags there (-fopenmp, -lgomp).
> Which is the preferred way to do it.
Either edit you CMakeCache.txt (e.g., "ccmake .") after setting up the cmake
build directory, or declare these as
> It is a protein, but the retrieved PDB was DNA structure.
You don't say what version of Open Babel you're using. Looking at the current
code for fastaformat.cpp, it should accept:
>protein
>peptide
>Protein
>Peptide
-Geoff
