Dear Amber users,
I am trying to reproduce the RESP charges of Ser for the Amber99 force
field.
In Tabel II of Cieplak et al. [J. Comput. Chem. 16, 1357 (1995)], the
authors listed the following MM minimized conformations for C5 (extended)
and aR (alpha helix) they used in RESP calculations. The angles with *
appear to be constrained during MM minimization although the authors did not
say that explicitly.
Phi Psi Chi-1 Chi2
C5 197 174 47 299
aR -60* -40* 187 43
I have tried five different calculations to reproduce the charges. Both
geometry optimization and charge fitting were performed at the level of
HF/6-31G* with the help of R.E.D. software
(
http://q4md-forcefieldtools.org/RED/). Two conformations were used with
RBRA (except B, which used QMRA) as described in the R.E.D. tutorial. The
P2N file for R.E.D. looks like this.
..
REMARK INTRA-MCC 0.0 | 1 12 13 14 2 8 | R => CH3CO
REMARK INTRA-MCC 0.0 | 6 11 7 16 17 18 | R => NHCH3
REMARK INTRA-MCC -0.4157 | 3 | K => N
REMARK INTRA-MCC 0.2719 | 9 | K => H
REMARK INTRA-MCC 0.5973 | 5 | K => C
REMARK INTRA-MCC -0.5679 | 10 | K => O
REMARK REORIENT 2 5 10 | 10 5 2 | 8 10 6 | 6 10 8 => C-C-O/O-C-C and
O-O-N/N-O-O
..
Here is the result for Ser. The values with * and ** deviate from those in
Amber99 FF by more than 0.03 and 0.05, respectively.
Atom
Amber99
A
B
C
D
E
CA
-0.0249
-0.0277
-0.0267
0.0169*
0.0122*
0.0053*
HA
0.0843
0.1112
0.1151*
0.0918
0.0893
0.0874
CB
0.2117
0.1585**
0.1327**
0.0676**
0.0861**
0.1512**
HB1
0.0352
0.0427
0.0496
0.0674*
0.063*
0.0377
HB2
0.0352
0.0427
0.0496
0.0674*
0.063*
0.0377
OG
-0.6546
-0.6215*
-0.6108*
-0.6159*
-0.6244*
-0.6074*
HG
0.4275
0.4085
0.4048
0.4193
0.425
0.4025
Amber99: Values listed in the Amber99 force field.
A: Bond angles and bond lengths were taken from the equilibrium values
listed in the Amber99 FF; All dihedral angles were fixed at the above values
for C5 and aR. No optimization performed.
B: Same as A but QMRA of Gaussian03 was used instead of RBRA of R.E.D.
C: The starting structures were the same as A but geometry optimization was
performed with Phi and Psi constrained only for aR. Chi's were allowed to
vary.
D: Same as C but Phi and Psi of both aR and C5 constrained. Chi's were
allowed to vary.
E: Same as C but all Phi, Psi, and Chi's were constrained for both C5 and
aR. In this case only the bond lengths and bond angles were allowed to vary.
Here are the questions.
1. Is there any protocol that one can use to reproduce the Amber99 charges
with a reasonable accuracy, say +/-0.05? Or what was wrong in my
calculations?
2. Is it OK to follow the procedure C to calculate RESP charges of
phosphoSer although the charges of "unphosphorylated" Ser do not agree with
the Amber99 FF? Can I use these values for phosphorylated Ser in MD
simulations that use the Amber99 FF? Homeyer et al. reported Amber FF
parameters for phosphoSer [J. Mol. Model 12, 281 (2006)] but I could not
find any comment on this issue.
Thanks,
Sanghwa Han
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Received on Mon Jan 12 2009 - 01:17:44 PST
