AMBER Archive (2009)

Subject: [AMBER] RE: VDW and TI for free energy

From: Ross Walker (
Date: Thu Oct 08 2009 - 19:43:48 CDT

Hi Qicun,

It's best to post such questions to the Amber mailing list which I am
copying on this reply. Please see for signup

> In the tutorial
> ( of
> pKa calculation, the VDW terms for disappearing proton attached to the
> oxygen in the
> hydroxyl of ASH are not changed. This is guaranteed by ff94 as you
> introduced,
> "Fortunately in the FF94 force field all protons attached to oxygen
> atoms were
> parameterized with a van oder Waals radius of zero."
> Which force field is the best for disappearing proton attached nitrogen
> in the protonated
> Lysine residue? Is any optimal force fields that are able to optimize
> the impact from such
> a disappearance of the charge of the proton to the minimum (if not
> zero)? I am using
> Amber 10.

The useful thing about making a proton disappear was indeed the fact that it
has zero VDW radii in the FF9X force field. If you plan to make another atom
disappear then you need to deal with the VDW changes as well. The best way
to address this is to use the softcore TI support in AMBER 10. Refer to
section 4.1.2 of the AMBER 10 manual (Page 102) for more details. There is
also a tutorial which covers this here:

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list