AMBER Archive (2002)

Subject: Fw: Valine to alanine Gibbs tutorial

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Mon Dec 16 2002 - 07:20:26 CST

Dear all,
I went thru the valine to alanine Gibbs tutorial in two variations in the
charges for the resulting atoms; first I used the
0.105 and zeros according to the tutorial, second, I used charge for alanine
as in lib files.

Can you tell me why in the tutorial is this - to me arbitrary - charge
value? Is the standard procedure to change the
perturbed-atom (say C-to-H) charges to their actual values or zeroes?

I got two results both of which differ from those in the tutorial (I put
them below). Moreover, in the 2nd case (which I think
is the correct one) even the sign is reversed! Could you tell me what;s
wrong?

Thank you.

All the best,

    Martin Lepsik

1st case:
Current Lambda = 0.000000
 Last F.E. update: Lambda = 0.000000 Step = 11000 Method = F.E.P.
 Accumulated "forward" quantities (Regular)
    Lam+d_lam = 0.100000 F_energy = 5.59082
    ELEC = 24.769 NONB = 1.324 14NB = 2.887
    14EL = -25.201 BADH = -0.148
 Accumulated "reverse" quantities (Regular)
    Lam-d_lam = 0.000000 F_energy = -5.10742
    ELEC = -25.078 NONB = -4.857 14NB = -3.274
    14EL = 25.592 BADH = 0.120

2nd case:
 Current Lambda = 0.000000
 Last F.E. update: Lambda = 0.000000 Step = 11000 Method = F.E.P.
 Accumulated "forward" quantities (Regular)
    Lam+d_lam = 0.100000 F_energy = -3.58055
    ELEC = 23.330 NONB = 0.275 14NB = 3.247
    14EL = -32.252 BADH = -0.127
 Accumulated "reverse" quantities (Regular)
    Lam-d_lam = 0.000000 F_energy = 4.76917
    ELEC = -23.653 NONB = -2.765 14NB = -3.258
    14EL = 32.580 BADH = 0.115

----------------------------------------------------------------------------
---------------------------------------------------------------------------- 

----
Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem