AMBER Archive (2009)

Subject: RE: [AMBER] Antechamber problem

From: 欧阳德方 (ouyangdf1978_at_hotmail.com)
Date: Fri Mar 27 2009 - 19:55:03 CDT

Thanks Junmei and Dave! You really help a lot.

Regards,
Ouyang

> Date: Fri, 27 Mar 2009 16:21:33 -0500
> Subject: Re: [AMBER] Antechamber problem
> From: junmwang_at_gmail.com
> To: amber_at_ambermd.org
>
> 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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_________________________________________________________________
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