[AMBER] antechamber

From: 闫玉娜 <hiyanyuna.gmail.com>
Date: Wed, 20 Aug 2014 10:31:10 +0800

Hi all,
I have a small molecule named 'HEM'. I want to use antechamber to build its
parameters. I use the command 'antechamber -i HEM_ideal.pdb -fi pdb -o
hem.mol2 -fo mol2 -c bcc -s 2 -nc 0'.But there are errors as follows:


“Running: /home/yanyuna/Programs/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac



Running: /home/yanyuna/Programs/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 305; net charge: 0
INFO: Number of electrons is odd: 305
      Please check the total charge (-nc flag) and spin multiplicity (-m
flag)

Running: /home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in -o
sqm.out" of bcc() in charge.c properly, exit”

I have attached its structure file. How can I solve it? Thank you


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Received on Tue Aug 19 2014 - 20:00:03 PDT
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