Dear Gromacs Users,
I am using plain cutoff for my 12-mer protein.
The grompp reports ARG to have a big charge group. this was also highlighted in
the following mail
http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html
I was just think if changing the charges on these atoms would help,
from
13 CT2 1 ARG CD 4 0.2 12.011 ; qtot 1.2
14 HA 1 ARG HD1 4 0.09 1.008 ; qtot 1.29
15 HA 1 ARG HD2 4 0.09 1.008 ; qtot 1.38
16 NC2 1 ARG NE 4 -0.7 14.007 ; qtot 0.68
17 HC 1 ARG HE 4 0.44 1.008 ; qtot 1.12
18 C 1 ARG CZ 4 0.64 12.011 ; qtot 1.76
19 NC2 1 ARG NH1 4 -0.8 14.007 ; qtot 0.96
20 HC 1 ARG HH11 4 0.46 1.008 ; qtot 1.42
21 HC 1 ARG HH12 4 0.46 1.008 ; qtot 1.88
22 NC2 1 ARG NH2 4 -0.8 14.007 ; qtot 1.08
23 HC 1 ARG HH21 4 0.46 1.008 ; qtot 1.54
24 HC 1 ARG HH22 4 0.46 1.008 ; qtot 2
to
CD 0.18
HD1 0.06
HD2 0.06
NE -0.7
HE 0.4
CZ 0.6
NH1 -0.8
HH11 0.5
HH12 0.5
NH2 -0.8
HH21 0.5
HH22 0.5
The above transformation of charges seems reasonable.
Would like to know if this is okay...
Best,
nahren
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