AMBER Archive (2006)

Subject: Re: AMBER: Ligand charge

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jan 05 2006 - 00:02:42 CST

Dear Bo,

As David pointed out in his email, u need to have a good charge scheme for
your ligand. Is it normal for your ligand, cholesterol, have a
total neutral charge? If not, u should follow the RESP protocol to get
the RESP charges for your ligand. Even if the total charge of your ligand
is zero, I would suggest to follow the RESP protocol and get the RESP
charges. As u might know, RESP protocol uses either GAUSSIAN or GAMESS,
which are doing quantum mechanical calculations on the system. But if
there is already a .prepi library file in literature, u can definitely use
that library for your ligand.

The other thing is the total time of your simulation. As pointed out by
David, u should not run a short simulation if you want to see what happens
to your ligand-protein system. A short simulation wont change the system
too much.

What I would suggest is to do some long simulations for your system with
different random seed numbers (the default IG is 71277. Run, for instance,
5 long simulations with different IG values). Use implicit solvent in your
system. I dont know how big your system is, but I once helped one of my
friend to do a simulation for a protein-ligand system. It was a normal
protein, not too big, but not too small either. I think for 1 ns it took
3-4 days to finish the job using 1 AMD Opteron CPU. U should run your
simulations in a time scale greater than 1 ns.

Good luck,

On Wed, 4 Jan 2006 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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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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