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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Received on Wed Apr 12 2017 - 08:00:02 PDT
