I am new to antechamber, I am trying to parameterize a macrocyclic compound, and am unable to get atom types or even coordinates in my output files, even using the sustiva_h.pdb tutorial example. It looks like a path problem to me, but Amber runs OK, so should I have additional lines in my .cshrc so that antechamber finds the parameters it is looking for?
I am providing the input line I used from the tutorial, and the output.
input:> antechamber -i sustiva_h-1.pdb -fi pdb -o sustiva_h.mol2 -fo mol2 -c bcc -s 2
output:
Running: /nmr/Programs/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 160; net charge: 0
Running: /nmr/Programs/amber/amber8/exe/divcon
Running: /nmr/Programs/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /nmr/Programs/amber/amber8/dat/antechamber/BCCPARM.DAT -j 4
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
This is the ANTECHAMBER_AC.AC file:
CHARGE 0.00 ( 0 )
Formula: H9 C14 N1 O2 F3 Cl1
ATOM 1 CL EFZ 1 0.000 0.000 0.000 0.000000 cl
ATOM 2 F1 EFZ 1 0.000 0.000 0.000 0.000000 f
ATOM 3 F2 EFZ 1 0.000 0.000 0.000 0.000000 f
ATOM 4 F3 EFZ 1 0.000 0.000 0.000 0.000000 f
ATOM 5 O1 EFZ 1 0.000 0.000 0.000 0.000000 os
ATOM 6 O2 EFZ 1 0.000 0.000 0.000 0.000000 os
ATOM 7 N EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 8 C1 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 9 C2 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 10 C3 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 11 C4 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 12 C5 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 13 C6 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 14 C7 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 15 C8 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 16 C9 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 17 C10 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 18 C11 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 19 C12 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 20 C13 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 21 C14 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 22 H122EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 23 H121EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 24 H112EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 25 H111EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 26 H101EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 27 HN EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 28 H5 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 29 H3 EFZ 1 0.000 0.000 0.000 0.000000 DU
ATOM 30 H2 EFZ 1 0.000 0.000 0.000 0.000000 DU
Thanks,
Tom Pochapsky
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Received on Mon Jan 09 2012 - 10:30:03 PST
