Dear all,
I am facing some problems relating charges derivation. I want to create a
force field for a modified aminoacid. Before doing so, I tried to recompute
the charges for lysine to see if I can recover the ones from the Amber
force fields, and not only I can't but I obtain different results depending
on the followed path.
I optimized lysine capped with CH3CO- and -NHCH3 in 2 different
conformations as in the J Comp Chem paper from 1995 by Cieplak et al. It
was done at the M06-2X/6-31+G** level of theory, and to be as close as
possible to the original paper I then manually assigned to the dihedrals
the values in Table 2 (differences between the optimized structures and the
tabulated values were small).
I obtained the gesp files from Gaussion09 C01 with the following inputs
(provided by antechamber with "antechamber -i LYS.pdb -fi pdb -o LYS.com
-fo gcrt -gv 1 -ge LYS.gesp"):
#P HF/6-31G* SCF=tight Pop=MK iop(6/33=2) iop(6/42=6) iop(6/50=1) Test
Units(Ang,Deg)
I then merged the 2 gesp files with a cat command.
I then tried 2 things (always fixing the charges of C/O/N/H atoms from main
chain):
1) "residuegen LYS.input" with LYS.input that was:
INPUT_FILE LYS.ac
CONF_NUM 2
ESP_FILE LYS.ESP
SEP_BOND N2 C4
SEP_BOND C2 N1
NET_CHARGE 1
ATOM_CHARGE N2 -0.347900
ATOM_CHARGE H1 0.274700
ATOM_CHARGE C2 0.734100
ATOM_CHARGE O1 -0.589400
PREP_FILE: LYS.prep
RESIDUE_FILE_NAME: LYS.res
RESIDUE_SYMBOL: LYS
2) with respgen and resp, with the following commands:
respgen -i LYS.ac -o LYS_Resp1.in -f resp1 -e 2 -a Constrains.dat -n 2
respgen -i LYS.ac -o LYS_Resp2.in -f resp2 -e 2 -a Constrains.dat -n 2
resp -O -i LYS_Resp1.in -o LYS_Resp1.out -e LYS.esp -q QIN -t qout_resp1
resp -O -i LYS_Resp2.in -o LYS_Resp2.out -e LYS.esp -q qout_resp1 -t
qout_resp2
antechamber -i LYS.ac -fi ac -o LYS_RESP.ac -fo ac -c rc -cf qout_resp2
Constraints.dat was :
CHARGE -0.347900 6 N2
CHARGE 0.274700 15 H1
CHARGE 0.734100 3 C2
CHARGE -0.589400 4 O1
// Cap on N
GROUP 6 0.00000
ATOM 7 C4
ATOM 8 C5
ATOM 14 O2
ATOM 23 H9
ATOM 24 H10
ATOM 25 H11
// Cap on C
GROUP 6 0.00000
ATOM 1 C1
ATOM 2 N1
ATOM 22 H8
ATOM 26 H12
ATOM 27 H13
ATOM 28 H14
// LYS
GROUP 22 1.00000
ATOM 3 C2
ATOM 4 O1
ATOM 5 C3
ATOM 6 N2
ATOM 9 C6
ATOM 10 C7
ATOM 11 C8
ATOM 12 C9
ATOM 13 N3
ATOM 15 H1
ATOM 16 H2
ATOM 17 H3
ATOM 18 H4
ATOM 19 H5
ATOM 20 H6
ATOM 21 H7
ATOM 29 H15
ATOM 30 H16
ATOM 31 H17
ATOM 32 H18
ATOM 33 H19
ATOM 34 H20
Here are the raw results (for atoms other than C/O/N/H from main chain):
AmberFF (1)Residuegen (2)Resp
Ca -0.2400 -0.1947 -0.2018
Cb -0.0094 -0.0552 -0.1125
Cg 0.0187 0.1093 0.1272
Cd -0.0479 -0.1474 -0.1514
Ce -0.0143 0.1073 0.1360
Nz -0.3854 -0.5148 -0.5388
Ha 0.1426 0.1195 0.1390
Hb 0.0362 0.0363 0.0539
Hg 0.0103 -0.0082 -0.0117
Hd 0.0621 0.0819 0.0794
He 0.1135 0.0951 0.0877
Hz 0.3400 0.3648 0.3707
And the differences between each method and the AmberFF charges:
(1)Residuegen (2)Resp
Ca 0.0453 0.0382
Cb -0.0458 -0.1031
Cg 0.0906 0.1085
Cd -0.0995 -0.1035
Ce 0.1216 0.1503
Nz -0.1294 -0.1534
Ha -0.0231 -0.0036
Hb 0.0001 0.0177
Hg -0.0185 -0.0220
Hd 0.0198 0.0173
He -0.0184 -0.0258
Nz 0.0248 0.0307
My problems are the following:
1) Why do I obtain different charges with the two methods? Which one is
recommended?
2) Charges on Cb/Cg/Cd/Ce/Nz are different by ~0.1e, up to 0.15 for Ce and
Nz with method (2). Do you think it is only due to the different Gaussian
versions that produces slightly different ESP? When differences are below
0.05e that's what I would have said, but 0.15e seems high to me. I am
puzzled by these results.
Thank you for your help,
Nicolas
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Received on Wed Oct 11 2017 - 03:30:03 PDT
