AMBER Archive (2004)

Subject: AMBER: LCPO parameters in gbsa

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Thu Feb 19 2004 - 10:53:56 CST

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.
Am I correct?
Thanks in advance
Giulio 

-- 

Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
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