*Dear Amber Users, *
*I want to simulate a protein structure docked with ADP and for ADP want to
generate its crd *
*and top files. In order to do so I used ANTECHAMBER to generate its
mol2 **file
calculate the charges and atom types. I used the following command. *
*root.drpunit-Precision-WorkStation-T3500:/home/drpunit/Desktop/interdomain/dockadp#
antechamber -i ADP.pdb -fi pdb -o adp.mol2 -fo mol2 -c bcc -s 2 *
*Running: /home/drpunit/amber12/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC
<
http://ANTECHAMBER_BOND_TYPE.AC> -f ac *
*Running: /home/drpunit/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC <
http://ANTECHAMBER_AC.AC> -p gaff *
*Total number of electrons: 205; net charge: 0 *
INFO: Number of electrons is odd: 205
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)
*Running: /home/drpunit/amber12/bin/sqm -O -i sqm.in <http://sqm.in> -o
sqm.out *
*Error: cannot run "/home/drpunit/amber12/bin/sqm -O -i sqm.in
<
http://sqm.in> -o sqm.out" of *
*bcc() in charge.c, properly**, exit *
Iam using Amber12 with Ambertools13.
also attaching the pdb files of the ligand and the complex.
what could be the possible reason.
Please guide.
Thanking in anticipation.
Regards,
Roopali
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Received on Wed Jun 03 2015 - 01:30:03 PDT
