[AMBER] error in antechamber

From: Nehad Elsalamouny <nehade.uow.edu.au>
Date: Sat, 12 Nov 2016 00:10:17 +0000

Dear Amber users,

I am trying to run antechamber for my ligand: antechamber -i hma.pdb -fi pdb -o hma.mol2 -fo mol2 -c bcc -s 2 -nc 1 -j 5

I get this error:

Running: /Users/Nehad/amber16/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /Users/Nehad/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 163; net charge: 1
INFO: Number of electrons is odd: 163
      Please check the total charge (-nc flag) and spin multiplicity (-m flag)

Running: /Users/Nehad/amber16/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/Users/Nehad/amber16/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

I don’t know what am I doing wrong!


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Received on Fri Nov 11 2016 - 16:30:03 PST
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