Hi everyone,
I don't have the OS around unfortunately to try it myself.
You could try to run [change -pf yes to -pf no first]
/Applications/Amber11/intel-mkl/bin/bondtype -j full \
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
manually and examine the output if it is wrong indeed (to rule out
some parsing errors). You could then try to nail it down further
by injecting 'printf()' statements around. Alternatively, I could
take a look if someone could give me a (temporary) shell at a leopard.
Best,
Volodymyr
On Tue, November 24, 2009 11:27, Ben Roberts wrote:
> Hi Scott,
>
> Last I knew, this problem still exists. It seems bondtype() was
> returning the wrong values for certain things.
>
> Specifically:
>
> <snip>
>
> ---Judge bond type for Residue 12 with ID of 11 and Name of THR ---
>
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic double)
> Error: cannot run "/Applications/Amber11/intel-mkl/bin/bondtype -j full
> -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
> Interestingly enough, it grumbles at a different point to Alan's
> original bug report.
>
> I'll see what I can find. Is there any indication as to what,
> technically speaking, is causing the problem?
>
> Ben
>
> Scott Brozell wrote:
>> Hi,
>>
>> What is the status of the antechamber tests on Uncia uncia ?
>> In particular, does the chemokine problem at the tail below still exist
>> ?
>>
>> thanks,
>> Scott
>
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Received on Tue Nov 24 2009 - 09:00:04 PST
