Thanks for your clarification. I have two other relating questions:
1. If I make a new residue file with a different atom type, which parameters for bond, angle, and dihedral involving the new atom type should be used? Can these parameters be copied to the new atom type by tleap when construting the prmtop file?
2. In fact, I am not very clear about the statement "We don't need to worry about removing the bonds, angles and dihedral terms as these are all internal to the residue and so the average properties of these terms should be identical in the model and protein systems. There is also no contribution from these terms to the derivative of the potential with respect to lambda." in the tutorial for pka calculation by TI method as in
http://ambermd.org/tutorials/advanced/tutorial6/section1.htm
Suppose the following Hamiltonian is used,
H(lambda) = lambda * H1 + (1-lambda) * H2, which H1 and H2 correspond to the protonated and unprotonated states, respectively.
If the bond, angle and dihedral/torsion interactions involving the disappeared hydrogen atom is not removed from the unprotonated state (prmtop), the derivative of the H(lambda) with respect to lambda (H1-H2) will also include the contribution from these terms. Why the tutorial says that "There is also no contribution from these terms to the derivative of the potential with respect to lambda." Do I understand it correctly?
Any suggestion is appreciated.
Many thanks.
Mingjun
--- 10年5月8日，周六, Carlos Simmerling <carlos.simmerling.gmail.com> 写道：
发件人: Carlos Simmerling <carlos.simmerling.gmail.com>
主题: Re: [AMBER] How to disable the VDW interaction?
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年5月8日,周六,下午6:01
1) the RADII section is for the intrinsic radius for the implicit
solvation calculations. it is not vdw radius.
2) the prmtop does not contain per-atom vdw parameters, only pointers
into the atom type arrays that hold the parameters. so, you can't
change 1 atom's parameters there, because you would have to change
them for all hydrogens of the same atom type.
3) it seems to me that you need to go back to the actual residue
library file and determine the atom type- some of the hydrogen atoms
in Amber's force fields already have zero for the vdw well depth (you
want that, not zero for radius). you need to check and see what it is,
and if it isn't zero then you will need to make a new residue file
with a different atom type that has zero for vdw interaction. it's nI ot
as simple as modifying the prmtop.
On Sat, May 8, 2010 at 2:51 AM, Jeffrey <jeffry20072008.yahoo.cn> wrote:
> Dear AMBER users,
>
> We are going to calculate the pka of a protonation of residue in a protein model, following the tutorial at http://ambermd.org/tutorials/advanced/tutorial6/. I disabled the vdw interaction by setting the vdw radii of the hydrogen atom to 0.0 in the prmtop file (the term under %FLAG RADII). But it is strange that the vdw interaction didn't change w/o modification of the radii.
>
> I am not sure whether I did it correctly or not and so request your suggestions.
>
> Many thanks.
>
> Jeffrey Yang
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat May 08 2010 - 06:00:04 PDT
