On Mon, Aug 02, 2010, Philippe Pinard wrote:
>
> When I do this command
> $AMBERHOME/exe/antechamber -i cen.pdb -fi pdb -o cen.prepin -fo prepi -c bcc -s
> 2 -nc 0
> I get this error message:
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
Did you do this? Are all the hydrogens present, and everything looks fine
visually?
> Error: cannot run "/opt/software/SGI/AMBER/amber9/exe/bondtype -i
I'd strongly recommend updating to AmberTools 1.4. It's certainly possible
that you are hitting some bug that has been fixed since 2006.
> Running: $AMBERHOME/exe/divcon
> /opt/software/SGI/intel/mkl/10.0.3.020/lib/em64t/libmkl_mc.so: undefined symbol:
> mkl_blas_xddot
Your version of divcon seems to be hosed. Again, the only simple thing to do
is upgrade.
....dac
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Received on Mon Aug 02 2010 - 19:00:04 PDT
