AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Sep 06 2006 - 16:16:58 CDT

I can add the H to the cAMP.pdb and save it into
another pdb file. However Antechamber still cannot
work with the new pdb file, the reason and the error
message is same as previous e-mail to you:

Error: cannot run "/home/local/amber9/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.ACO -o ANTECHAMBER_BOND_TYPE.AC
-f ac -j full" in judgebondtype () of antechamber.c
properly, exit.

Will you please tell me how to solve this problewm?

Best regards.

Fenghui Fan

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Tue, Sep 05, 2006, Fenghui Fan wrote:
> >
> > I have the cAMP ligand pdb file:
> >
> > Error: cannot run "/home/localamber9/exebondtype
> -i
> > ANTECHAMBER_BOND_TYPE.ACO -o
> ANTECHAMBER_BOND_TYPE.AC
> > -f ac -j full: in judgebondtype () of
> antechamber.c
> > properly, exit
>
> This error has already been explained in earlier
> e-mails, so it is not
> necessary to repeat the question. (Your next
> comment indicates that you
> understood that the problem was that your ligand
> does not have hydrogens.)
>
> >
> > I also try to use xleap to add the H to the cAMP,
> > however xleap cannot do that because there is no
> cAMP
> > residue.
>
> You don't need a residue library to use xleap to add
> hydrogens. Here is a
> general procedure: Use "loadPdb" to read the file,
> "bondbydistance" to get
> initial bonds. Then you can draw in the hydrogens
> you need by hand, and use
> "relax selection" to clean them up. Or, you can
> mark the all of the bonds in
> the purine ring as "aromatic" (click on them three
> times), and use "Add H and
> build". This will do a pretty reasonable job,
> although you will probably
> want to erase the one of the hydrogens that it adds
> to the phosphate oxygens.
>
> The above is only an outline; you will probably have
> to play with things a bit
> to get just what you want.
>
> There are other programs that will more
> automatically add hydrogens to a
> structure; since what you have is a very common
> molecule, you might also be
> able to find a protonated version on the web
> somewhere.
>
> ....dac
>
>
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