Hi,
I am using Amber9 and have installed AmberTools 1.3and have set the
following in the bashrc file as suggested by the ambergroup :
export AMBERHOME=/root/amber11
export PATH=$AMBERHOME/bin\:/root/amber9/exe\:$PATH
For the antechamber tutorial, the command and the output were as follows:
$antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s
2
Running: /root/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /root/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 160; net charge: 0
Running: /root/amber11/bin/*sqm* -O -i *sqm.in* -o *sqm.out*
Running: /root/amber11/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p /root/amber11/dat/antechamber/BCCPARM.DAT -s
2 -j 1
Running: /root/amber11/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC
However as given in the tutorial,
mopac.in, mopac.out, mopac.pdb
are not created instead sqm.in and sqm.out are created. Is my protocol
correct? Moreover how to analyse sqm.in and sqm.out ?
Plz help.
Thanks,
Asfa.
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Received on Tue Apr 06 2010 - 01:00:02 PDT
