AMBER Archive (2009)

Subject: Re: [AMBER] failure to run antechamber with amber 10

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jan 30 2009 - 02:04:33 CST

Apologies. Although that was the only error output, and Amber9 worked
nicely, I should have carried out tests with Amber10 before posting.

As soon as there is space (a long procedure with NWChem is under way),
I'll first verify that antechamber tests still pass, as they passed
after installation.

Should I find the problem persisting, I would be glad to furnish the
input file. However, as it deals of an unreported compound of a new
class under study, I would prefer to furnish the file on a private
basis (although I don't expect it will be great science). After
publican (if and when) it could be made public.

Thanks
francesco

On Thu, Jan 29, 2009 at 11:45 PM, David A. Case
<case_at_biomaps.rutgers.edu> wrote:
> On Thu, Jan 29, 2009, Francesco Pietra wrote:
>
>>
>> with amber10/ambertools 1.2 i was unable to run antechamber, as
>> indicated below (i can't remember if this is the 1st time i am dealing
>> with antechamber in ambertools 1.2)
>>
>>
>>
>> $AMBERHOME/exe/antechamber -i myfile.pdb -fi pdb -o myfile.prepin -fo
>> prepi -c bcc -s 2
>>
>> returned the error:
>>
>> Error: cannot run "/usr/local/amber10/bin/bondtype -j full -i
>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
>> judgebondtype() of antechamber.c properly, exit
>> Running: /usr/local/amber10/bin/bondtype -j full -i
>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Is this the *only* output/error? Usually, other things are printed
> which suggest the origin of the problem.
>
> I'm assuming that the antechamber test cases all pass. That strongly
> implies that there is something about myfile.pdb that is leading to
> problems that are not be caught by the test suite. But since we don't
> have access to your particular input file, it's unclear what sort of
> help you are really expecting.
>
> Of course, having an actual example of something that (seems to) work in
> Amber 9 but fails in Amber10 (i.e. a regression) would be of interest.
>
> [You're pretty experienced with both Amber and this mailing list; you
> should already appreciate the points raised above.]
>
> ...dac
>
>
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