AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber problem

From: Junmei Wang (junmwang_at_gmail.com)
Date: Fri Mar 27 2009 - 16:21:33 CDT

Hi, Ouyang,

There is a problem with your molecule. The atom H21 should be carbon, not
hydrogen. If you change the atom name to C21, antechamber should work fine.

Best

Junmei

2009/3/26 欧阳德方 <ouyangdf1978_at_hotmail.com>

>
>
>
>
> Dear all,
>
> When I run antechamber of AMBER9 to deal with my pdb file, there is one
> problem. I attached my pdb file. The command:
>
> antechamber -nc 4 -i 4+arginine.pdb -fi pdb -o 4+arginine.prepin -fo prepi
> -c bcc
>
> The problems:
> "For atom[33]:O, the best APS is not zero, exit
> Warning: the assigned bond types may be wrong, 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
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly
> increase the computer time
> Error: cannot run "/usr/local/amber9/exe/bondtype -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
> judgebondtype() of antechamber.c properly, exit"
>
> I try to find answers from previous post, such as
> http://archive.ambermd.org/200709/0042.html
> http://archive.ambermd.org/200708/0471.html
> http://archive.ambermd.org/200801/0240.html.
>
> I try the different approaches above mentioned,
> antechamber -fi pdb -fo mol2 -i 4+arginine.pdb -o 4+arginine.mol2 -j 5
> but when I try to use mol2 file or ANTECHAMBER_BOND_TYPE.AC as input file,
> the same mistake happens.
>
> Maybe the same problem still exists in the mol2 file and
> ANTECHAMBER_BOND_TYPE.AC, but I donot know how to fix it.
> If it isnot, how can I do?
>
> Thanks,
> Ouyang
>
>
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