AMBER Archive (2006)

Subject: AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it?

From: a a (patd_2_at_hotmail.com)
Date: Mon Nov 27 2006 - 02:50:12 CST

Dear All,

I got a drug with the following structure, (overall charge = 0)

N(C3H7)3

however, whenever I run the antechamber, the following error message
appears:

antechamber -i test2.pdb -fi pdb -o test2.prepin -fo prepi -c bcc -s 2

Running: /home/cmche/amber8/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 82; net charge: 0

Running: /home/cmche/amber8/amber8/exe/divcon

Running: /home/cmche/amber8/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC
-o ANTECHAMBER_AM1BCC.AC -f ac -p
/home/cmche/amber8/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

Running: /home/cmche/amber8/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
ANTECHAMBER_PREP.AC -p gaff

Running: /home/cmche/amber8/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC -f int
-o test2.prepin -rn "TTC " -rf molecule.res

It seems to me that antechamber did not support tertary amines? Am I
correct? How can I overcomes this error?

Best regards,

Annie

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