Hi,
I am trying to use antechamber for a drug, which works great for one molecule, but if I use a pdb with two copies of the molecule, antechamber never ends:
antechamber -i ritonavir_2mol.pdb -fi pdb -o ritonavir_2mol.mol2 -fo mol2 -c bcc -s 2
Running: /Users/fabian/TOOLS/amber/amber12/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
---Judge bond type for Residue 1 with ID of 1 and Name of RIT ---
---Judge bond type for Residue 2 with ID of 2 and Name of RIT ---
Running: /Users/fabian/TOOLS/amber/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 768; net charge: 0
Running: /Users/fabian/TOOLS/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out
What is the right approach for this problem?
Best regards,
Fabian
_______________________________
Fabian Glaser, PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
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Received on Thu Mar 27 2014 - 06:00:02 PDT
