AMBER Archive (2005)

Subject: Re: AMBER: Antechamber error

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Oct 25 2005 - 19:16:20 CDT

hi,
  I further looked into the problem by inspecting the ANTECHAMBER_AC.AC0 file.
It looks smthg like this:

CHARGE 0.00 ( 0 )
Formula: H44 C23 O5
ATOM 1 C01 DAG 0 0.000 0.000 0.000 0.000000 C01
ATOM 2 H20 DAG 0 0.000 0.000 0.000 0.000000 H20
ATOM 3 H21 DAG 0 0.000 0.000 0.000 0.000000 H21
ATOM 4 H22 DAG 0 0.000 0.000 0.000 0.000000 H22
ATOM 5 C02 DAG 0 0.000 0.000 0.000 0.000000 C02
ATOM 6 H23 DAG 0 0.000 0.000 0.000 0.000000 H23
ATOM 7 H24 DAG 0 0.000 0.000 0.000 0.000000 H24
ATOM 8 C03 DAG 0 0.000 0.000 0.000 0.000000 C03
ATOM 9 H25 DAG 0 0.000 0.000 0.000 0.000000 H25
ATOM 10 H26 DAG 0 0.000 0.000 0.000 0.000000 H26
ATOM 11 C04 DAG 0 0.000 0.000 0.000 0.000000 C04
ATOM 12 H27 DAG 0 0.000 0.000 0.000 0.000000 H27
ATOM 13 H28 DAG 0 0.000 0.000 0.000 0.000000 H28
ATOM 14 C05 DAG 0 0.000 0.000 0.000 0.000000 C05
ATOM 15 H29 DAG 0 0.000 0.000 0.000 0.000000 H29
ATOM 16 H30 DAG 0 0.000 0.000 0.000 0.000000 H30
ATOM 17 C06 DAG 0 0.000 0.000 0.000 0.000000 C06
ATOM 18 H31 DAG 0 0.000 0.000 0.000 0.000000 H31
ATOM 19 H32 DAG 0 0.000 0.000 0.000 0.000000 H32
ATOM 20 C07 DAG 0 0.000 0.000 0.000 0.000000 C07
ATOM 21 H33 DAG 0 0.000 0.000 0.000 0.000000 H33
ATOM 22 H34 DAG 0 0.000 0.000 0.000 0.000000 H34
ATOM 23 C08 DAG 0 0.000 0.000 0.000 0.000000 C08
ATOM 24 H35 DAG 0 0.000 0.000 0.000 0.000000 H35
ATOM 25 H36 DAG 0 0.000 0.000 0.000 0.000000 H36
ATOM 26 C09 DAG 0 0.000 0.000 0.000 0.000000 C09

Further more there is no BOND information at the end of the file,
which is usually there.

So even atomtype would not run correctly on this.

Any help would be appreciated. PDB file is attached with the last mail
in this thread.
Thanks
Nitin
On 10/25/05, Nitin Bhardwaj <nbhardwaj_at_gmail.com> wrote:
> Dear Amber users,
> 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
> ******************
>
> I checked my structure for valency and bond requirements. Everything
> seems fine.
> So it does not make sense to adjust the valence penalty parameters or
> increase MAXVASTATE.
>
> I am attaching my PDB file.
> Has anyone encountered this problem before?
> Any help woud be greatly appreciated.
> thanks
> Nitin
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