Thank you so much. No idea where that proton came from, it's not
supposed to be there!
On 12/13/2016 03:33 PM, Bruno Falcone wrote:
> Hi, sorry to jump in the conversation but hope I can be of any use.
>
> The problem I can see is that you set the charge to be 0 whereas it is
> +1 since you have a protonated nitrogen in the aliphatic ring.
>
> I ran antechamber with the +1 charge and I obtained the structure
> attached.
>
> Regards.
>
> Bruno
>
> On 13/12/16 11:14, Andreas Tosstorff wrote:
>> Hi David,
>>
>> this is the command line and output:
>>
>> antechamber -i L01.pdb -fi pdb -o L01.mol2 -fo mol2 -c bcc
>> Total number of electrons: 195; net charge: 0
>> INFO: Number of electrons is odd: 195
>> Please check the total charge (-nc flag) and spin multiplicity
>> (-m flag)
>>
>> Running: /share/apps/amber16/bin/sqm -O -i sqm.in -o sqm.out
>> Error: cannot run "/share/apps/amber16/bin/sqm -O -i sqm.in -o sqm.out"
>> of bcc() in charge.c properly, exit
>>
>> It works fine when not using the -c flag:
>>
>> antechamber -i L01.pdb -fi pdb -o L01.mol2 -fo mol2
>>
>>
>> On 12/13/2016 03:07 PM, David A Case wrote:
>>> On Tue, Dec 13, 2016, Andreas Tosstorff wrote:
>>>> 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.
>>> What is the *exact* command line you used? This is what is needed:
>>>
>>> antechamber -i <pdbfile> -fi pdb -o <mol2file> -fo mol2
>>>
>>> Also: do the antechamber tests pass? The most likely explanation I
>>> can see is
>>> that you are not really calling antechamber or acdoctor correctly,
>>> or that you
>>> are giving it an empty or corrupted PDB file. Have you run
>>> antechamber on
>>> other inputs?
>>>
>>> ....dac
>>>
>>>
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>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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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 - 07:00:03 PST
