AMBER Archive (2006)

Subject: Re: AMBER: Ligand charge

From: David Mobley (dmobley_at_gmail.com)
Date: Wed Jan 04 2006 - 13:43:54 CST

Ligand partial charges will almost certainly significantly affect the
orientation of a ligand in a binding site. In fact, the longer you run MD,
the more significant the results can be. If your simulation is really short,
the ligand will stay almost in the same orientation in which it starts out.
On long timescales, it has time to change orientations significantly and the
charges can have more effect.

If you are trying to identify the ligand bound orientation this may not be
the best way to do it. In my experience it can take 1 ns or more for ligands
to change orientations in some binding sites, meaning that even if you start
the ligand in the wrong orientation it may not find the correct one within 1
ns.

Aside from the fact that partial charges will make a difference in the
orientation, you *have* to have ligand partial charges to be able to run MD,
unless you assume it's uncharged and the only thing that matters is sterics,
which is a rather strange thing to do.

Since you're at UCSF, too, you could come by and we could talk about this
sometime. I'm in Genentech Hall in the Dill lab area; my desk is across from
N474E.

David Mobley

On 1/4/06, bybaker_at_itsa.ucsf.edu <bybaker_at_itsa.ucsf.edu> wrote:
>
> Dear Ilyas and Pawel:
>
> Thank you very much for your helps.
>
>
> >Then use antechamber to create the .prep file. Here, it is important what
> >kind of a charge method you are using. As an example;
>
> >antechamber -i chol3_new.pdb -fi pdb -o chol3_new.prepi -fo prepi -c bcc
> >-nc 0 -at gaff
>
> >will use the bcc charge method, and the gaff atom types. If you have the
> >charges for each atom in the 'chol' molecule in a file, u can give that
> >file explicitely, too, using antechamber.
>
> The ligand, a cholesterol here, has 0 net-charge according to 'xleap'. I
> am not sure if I need to work out the partial atomic charge for the
> lignad. I only want to subject the system (protein and ligand) to
> minimization and a short MD. So I can have rough idea on how the
> cholesterol located inside the protein. In this case, how necessary to
> care about the ligand charge statue?
>
> Thank you for any advices.
>
> All the best
>
> Bo
>
>
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