AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 05 2006 - 15:55:26 CDT

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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