AMBER Archive (2004)

Subject: Re: AMBER: LCPO parameters in gbsa

From: David A. Case (
Date: Mon Feb 23 2004 - 12:51:46 CST

On Thu, Feb 19, 2004, Giulio Rastelli wrote:

> I just compared the LCPO values in mdread.f with the original values
> in the original paper (J Comput Chem 1999, 20, 217) and found that
> the N-sp3 values are assigned to the N3 atom type only:
> else if (atype.eq.'N3') then
> if (nbond.eq.1) then
> x(L165-1+i) = 1.65d0 + 1.4d0
> x(L170-1+i) = 0.078602d0
> x(L175-1+i) = -0.29198d0
> x(L180-1+i) = -0.0006537d0
> x(L185-1+i) = 0.00036247d0
> else if (nbond.eq.2) then
> etc.....
> since N3 is a protonated nitrogen, I think the N-sp3 LCPO parameters
> should rather be assigned to the NT atom type, or both.

This looks OK to me(?). A protonated nitrogen like N3 should have
N-sp3 parameters, as far as I can see. The NT atom type seems only to
be used for deprotonated lysine residues. Your guess is probably as
good as mine about what size parameters such a deprotonated amine should have.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to