AMBER Archive (2009)

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

Date: Sat Oct 10 2009 - 03:44:31 CDT

Hi Qicun,

> *(1) For OH all FF9X VDW radius is zero, including FF02 or latest version,
> right?*

the hydrogen type HO in ff99 (and later ones I believe) has a vdw radius
of zero. If you want to make sure, take a look at the parmXX.dat you load
when building your system, it has the vdW-parameters at the end (the files
are in $AMBERHOME/dat/leap/parm/).

> *(2) Generally, is it right, using R-XH as an example, that*
> * disappearing charge R-XH -> R-X^-(p0) is different from *
> * disappearing atom (charge + mass) R-XH -> R-X(^-)*
> * (p0 is proton mass with zero charge and **X^- an anion of X)?*

In the limit of enough sampling, having the chargeless, interactionsless
mass p0 attached to an atom should not change your system behaviour. You
would however get different free energy results from the two processes you
describe, because in one of them, you also remove the bond potential of
the H-X bond from the system. This is a contribution that should cancel
out if you do the other leg of your free energy cycle the same way though.

So in principle the two ways to remove a hydrogen should give the same
final answer, but possibly different intermediate results.



Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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