Hi there,
I have this molecule:
HETATM 759 O1 MOL 1 30.900 25.892 20.427 1.00 0.00
HETATM 760 N1 MOL 1 31.331 26.323 21.712 1.00 0.00
HETATM 761 O2 MOL 1 30.655 27.390 22.350 1.00 0.00
HETATM 762 C1 MOL 1 32.091 25.503 22.441 1.00 0.00
HETATM 763 C2 MOL 1 31.844 25.301 23.730 1.00 0.00
HETATM 764 H1 MOL 1 30.874 25.361 24.226 1.00 0.00
HETATM 765 N2 MOL 1 33.000 24.989 24.302 1.00 0.00
HETATM 766 C3 MOL 1 33.938 24.991 23.361 1.00 0.00
HETATM 767 C4 MOL 1 35.434 24.817 23.685 1.00 0.00
HETATM 768 N3 MOL 1 33.383 25.279 22.180 1.00 0.00
HETATM 769 C5 MOL 1 34.050 25.098 20.854 1.00 0.00
HETATM 770 C6 MOL 1 34.970 26.276 20.500 1.00 0.00
HETATM 771 O3 MOL 1 34.178 27.330 19.950 1.00 0.00
HETATM 772 H2 MOL 1 34.118 28.084 20.607 1.00 0.00
HETATM 773 H3 MOL 1 33.261 25.049 20.104 1.00 0.00
HETATM 774 H4 MOL 1 34.640 24.182 20.894 1.00 0.00
HETATM 775 H5 MOL 1 35.756 26.002 19.796 1.00 0.00
HETATM 776 H6 MOL 1 35.433 26.666 21.407 1.00 0.00
HETATM 777 H7 MOL 1 36.170 24.824 22.882 1.00 0.00
HETATM 778 H8 MOL 1 35.756 24.686 24.719 1.00 0.00
That is converted to mol2 with babel 2.2.3
and the I do:
antechamber -i mol1.mol2 -fi mol2 -o mol1_bcc_gaff.mol2 -fo mol2 -c bcc -nc
0 -m 1 -s 2 -df 2 -at gaff -pf n
Info: Bond types are assigned for valence state 1 with penalty of 1
Total number of electrons: 89; net charge: 0
INFO: Number of electrons is odd: 89
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)
Running: /Users/alan/Programmes/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/Users/alan/Programmes/amber11/bin/sqm -O -i sqm.in -o
sqm.out" of bcc() in charge.c properly, exit
Running: /Users/alan/Programmes/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /Users/alan/Programmes/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p gaff
I do believe the molecule has net charge 0, but ... otherwise, what else can
I do here?
Many thanks in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 12 2010 - 07:30:04 PDT
