Your command seems OK.
Check sqm.out, does it give a more informative message? Are you sure the
starting structure is OK?
Hope this helps,
Bruno
On 18/08/16 15:53, ATUL KUMAR wrote:
> Dear Urers,
> I am using antechamber for generating atomic charges and parameters for a
> ligand(Net charge is -4) molecules by the following command:
>
> antechamber -i Mol_red5.pdb -fi pdb -o Mol_red5.mol2 -fo mol2 -c bcc -s 2
> -nc -4
>
> after funning this i am getting following error message:
>
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 422; net charge: -4
>
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i sqm.in
> -o sqm.out" of bcc() in charge.c properly, exit
>
> Please help me out with this.
>
> *Atul Kuamr jaiswal*
> Research Scholar
> School of Computational and Integrative Sciences
> Centre for Computational Biology and Bioinformatics (CCBB)
> JNU,New Delhi
> India.
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Received on Thu Aug 18 2016 - 13:00:02 PDT
