AMBER Archive (2009)

Subject: Re: [AMBER] charged or not

• Previous message: Andrew Olson: "[AMBER] Antechamber prep question"
• In reply to: s. Bill: "[AMBER] charged or not"
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On Thu, Jul 09, 2009, s. Bill wrote:

> I am new AMBER user and I am working on simulating a carboxylate ligand
> with a protein.
> During defining the carboxylate ligand as a non-standard residue (using
> Antechamber), I defiend it as carboxlic acid (where there is no atom
> type for the charged oxygen), is this right?

Generally, carboxylates are charged, but this is not always the case. You
will have to decide whether or not to build your ligand in the neutral or in
the anionic form.

> but, now when I loaded my pdb file, xleap will add hydrogen,
> subsequently, it will add hydrogen to the my ligand's oxygen.

LEaP only adds hydrogens that are present in the library (which you will make)
and which are *not* present in the input PDB file. Always check the prmtop
file itself to make sure that LEaP did what you wanted it to do.

...hope this helps....dac

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• Previous message: Andrew Olson: "[AMBER] Antechamber prep question"
• In reply to: s. Bill: "[AMBER] charged or not"
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