Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence

From: Andreas Tosstorff <>
Date: Tue, 13 Dec 2016 10:01:37 +0100

I tried to run acdoctor also on my own system now with the same error. I
attached the pdb file to this mail. There are no AC* files being generated.



gnu compiler

On 12/13/2016 09:40 AM, Andreas Tosstorff wrote:
> 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 -o
> -p gaff
> Cannot open the ac input file:, exit
> Error: cannot run "/share/apps/amber16/bin/atomtype -i
> -o -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
>> _______________________________________________
>> AMBER mailing list

M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Tel.: +49 89 2180 77059

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Received on Tue Dec 13 2016 - 01:30:03 PST
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