Dear David,
thanks for your response.
I am running Ambertools16 on CentOS. I am not sure on the compiler,
since I run this on a remote system and I did not install Amber myself
myself. Any suggestion on how to check for this? I am currently
installing AmberTools on my own system to see if I can reproduce the error.
I also receive this error message:
Running: /share/apps/amber16/bin/atomtype -i ACDOCTOR_BOND.ac -o
ACDOCTOR_ATOM.ac -p gaff
Cannot open the ac input file: ACDOCTOR_BOND.ac, exit
Error: cannot run "/share/apps/amber16/bin/atomtype -i ACDOCTOR_BOND.ac
-o ACDOCTOR_ATOM.ac -p gaff" in main() of antechamber.c properly, exit
Kind regards,
Andreas
On 12/12/2016 05:27 PM, David A Case wrote:
> On Mon, Dec 12, 2016, Andreas Tosstorff wrote:
>> I am trying to prepare a ligand with antechamber. The job fails and
>> acdoctor states:
>>
>> "Warning: There are no hydrogen and halogens in this molecule, it is
>> highly possible that this molecule has open valence"
> I cannot reproduce your result: acdoctor doesn't report any errors for me.
> And antehcamber works fine, giving atom types that look fine, and not having
> troubles with hydrogens. Please double check that no "operator error" is
> involved here, i.e. that you are loading the file you intended to load.
> Examine any AC* files that are created.
>
> Which version of AmberTools are you using? Try AmberTools16 if you are not
> already doing so (although I don't see why that should make a difference.)
> If you still can't figure it out, post your input pdb as an attachment:
> putting in in-line in emails often causes it to get mangled.
> Also, indicate which OS and compiler you are using.
>
> ....dac
>
>
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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Tue Dec 13 2016 - 01:00:02 PST
