Hello,
The molecule seems symmetric. Thus, atomic charges should at some point
reflect that.
A quick workaround here could be to generate a residue from one generic
unit and build the full cycle with tleap.
residuegen won't help here since there are 4 bonds between units, but
respgen+prepgen should do the work.
Gerald.
On 04/12/2017 04:47 PM, David Case wrote:
> On Wed, Apr 12, 2017, Maura Malinska wrote:
>>
>> I try to generate mol2 file using antechamber. Command below:
>> antechamber -i CB6.pdb -fi pdb -o CB6.mol2 -fo mol2 -c bcc -s 2
>>
>> It's giving me standard respond:
>> Running: /home/mauram/amber16/bin/bondtype -j full -i
>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>>
>> Running: /home/mauram/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
>> ANTECHAMBER_AC.AC -p gaff
>> Total number of electrons: 516; net charge: 0
>>
>> Running: /home/mauram/amber16/bin/sqm -O -i sqm.in -o sqm.out
>>
>> But then multitude of lines like this shows up and program stops:
>> Info: the number of the path atoms exceeds MAXPATHATOMNUM(145000) for
>> atom[32],extend the size and reallocate the memory automatically
>
> I can confirm the problem. Antechamber runs fine if you don't ask for
> bcc charges, but gets lost in the cyclic molecule in assigning bond types
> during the bcc procedure.
>
> Not sure if any the SAMPL5 folks have run across this. I'm looking for a
> workaround, and will post anything I find here.
>
> ....dac
>
>
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>
--
____________________________________________________________________________
Prof. Gerald MONARD
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Université de Lorraine
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e-mail : Gerald.Monard.univ-lorraine.fr
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Received on Wed Apr 12 2017 - 08:30:03 PDT
