On Tue, Oct 25, 2005, Nitin Bhardwaj wrote:
> When I run antechamber to prepare *.prepin file, I say:
>
> antechamber -i dag2.pdb -fi pdb -o dag.prepin -fo prepi -c bcc -s 2
>
> It says:
>
> *****************
> Running: /sprog/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 358; net charge: 0
>
> Running: /sprog/amber8/exe/divcon
>
> Running: /sprog/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> ANTECHAMBER_AM1BCC.AC -f ac -p
> /sprog/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
> ******************
Try adding "-j 5" to your antechamber run.
>
> I am attaching my PDB file.
I may have missed something, but it doesn't seem to be there.
....good luck...dac
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Received on Thu Nov 03 2005 - 23:53:02 PST
