AMBER Archive (2009)

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

From: Qicun Shi (qshi01_at_gmail.com)
Date: Fri Oct 09 2009 - 21:00:08 CDT

*Hi Ross:*
**
*Thanks for the mesages.*
**
*(1) For OH all FF9X VDW radius is zero, including FF02 or latest version,
right?*
**
*(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)?*
**
*Qicun*
**
*> In the tutorial *
*> (http://ambermd.org/tutorials/advanced/tutorial6/section1.htm) 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:
http://ambermd.org/tutorials/advanced/tutorial9/

Good luck,
Ross

/\
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|\oss Walker
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