Hi,
I used antechamber to generate charges for my ligand. However, for some
reason when I select gaff for atom type I get different charges than gaff2.
Is that normal or I am doing something wrong?
For gaff I use:
antechamber -i igp.mol2 -fi mol2 -o igp.prepc -fo prepc -nc -2 -c bcc -s 2
-at gaff
the prepc file
4 C1 c3 M 47.425000 28.343000 12.188000 0.154400
5 OP4 os S 47.571000 28.101000 10.791000 -0.595200
6 P p5 3 47.809000 29.365000 9.807000 1.346900
7 OP1 o E 49.010000 30.110000 10.366000 -0.733833
8 OP2 o E 46.514000 30.167000 9.845000 -0.733833
9 OP3 o E 48.084000 28.765000 8.440000 -0.733833
10 H11 h1 E 46.542000 27.751000 12.514000 0.042700
11 H12 h1 E 47.198000 29.404000 12.467000 0.042700
12 C2 c3 M 48.699000 27.871000 12.860000 0.095100
13 O2 oh S 49.775000 28.702000 12.404000 -0.651800
14 H4 ho E 49.515000 28.929000 11.412000 0.441000
15 H2 h1 E 48.919000 26.824000 12.546000 0.065700
16 C3 c3 M 48.649000 27.906000 14.394000 0.231300
17 O3 oh S 47.506000 27.158000 14.774000 -0.643800
18 H5 ho E 46.961000 27.560000 15.559000 0.400000
19 H3 h1 E 48.671000 28.996000 14.630000 0.046700
20 CG cc M 49.934000 27.291000 14.799000 -0.387400
21 CD1 cd B 51.057000 28.021000 15.148000 -0.231100
22 NE1 na B 52.063000 27.118000 15.384000 -0.197400
23 CE2 ca S 51.660000 25.838000 15.181000 -0.126200
24 CZ2 ca S 52.274000 24.597000 15.276000 -0.154000
25 HZ2 ha E 53.323000 24.553000 15.559000 0.087000
26 HE1 hn E 53.017000 27.428000 15.680000 0.251700
27 HD1 h4 E 51.169000 29.102000 15.222000 0.238000
28 CD2 ca M 50.246000 25.860000 14.761000 -0.002800
29 CE3 ca M 49.540000 24.702000 14.495000 -0.154000
30 HE3 ha E 48.499000 24.740000 14.184000 0.110000
31 CZ3 ca M 50.205000 23.485000 14.611000 -0.164000
32 HZ3 ha E 49.667000 22.569000 14.377000 0.082000
33 CH2 ca M 51.546000 23.432000 15.000000 -0.207000
34 HH2 ha E 52.049000 22.472000 15.089000 0.081000
And for gaff2 using the same mol2 file and just change -at
antechamber -i igp.mol2 -fi mol2 -o igp.prepc -fo prepc -nc -2 -c bcc -s 2
-at gaff2
4 C1 c3 M 47.425000 28.343000 12.188000 0.195400
5 OP4 os S 47.571000 28.101000 10.791000 -0.574200
6 P p5 3 47.809000 29.365000 9.807000 1.331900
7 OP1 o E 49.010000 30.110000 10.366000 -0.927167
8 OP2 o E 46.514000 30.167000 9.845000 -0.927167
9 OP3 o E 48.084000 28.765000 8.440000 -0.927167
10 H11 h1 E 46.542000 27.751000 12.514000 -0.011300
11 H12 h1 E 47.198000 29.404000 12.467000 -0.011300
12 C2 c3 M 48.699000 27.871000 12.860000 0.100100
13 O2 oh S 49.775000 28.702000 12.404000 -0.655800
14 H4 ho E 49.515000 28.929000 11.412000 0.472000
15 H2 h1 E 48.919000 26.824000 12.546000 0.018700
16 C3 c3 M 48.649000 27.906000 14.394000 0.127300
17 O3 oh S 47.506000 27.158000 14.774000 -0.640800
18 H5 ho E 46.961000 27.560000 15.559000 0.404000
19 H3 h1 E 48.671000 28.996000 14.630000 0.159700
20 CG cc M 49.934000 27.291000 14.799000 -0.117400
21 CD1 cd B 51.057000 28.021000 15.148000 -0.072100
22 NE1 na B 52.063000 27.118000 15.384000 -0.204400
23 CE2 ca S 51.660000 25.838000 15.181000 -0.081200
24 CZ2 ca S 52.274000 24.597000 15.276000 -0.164000
25 HZ2 ha E 53.323000 24.553000 15.559000 0.099000
26 HE1 hn E 53.017000 27.428000 15.680000 0.270700
27 HD1 h4 E 51.169000 29.102000 15.222000 0.283000
28 CD2 ca M 50.246000 25.860000 14.761000 -0.043800
29 CE3 ca M 49.540000 24.702000 14.495000 -0.080000
30 HE3 ha E 48.499000 24.740000 14.184000 0.145000
31 CZ3 ca M 50.205000 23.485000 14.611000 -0.193000
32 HZ3 ha E 49.667000 22.569000 14.377000 0.095000
33 CH2 ca M 51.546000 23.432000 15.000000 -0.160000
34 HH2 ha E 52.049000 22.472000 15.089000 0.090000
The atom types and coordinates (if it matters at all) are identical however
the overall charge of the phosphate group in gaff2 is significantly more
negative.
I would appreciate any help and explanation.
Thanks
Yuliana
--
Yuliana Bosken
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Received on Sat Jul 28 2018 - 16:00:02 PDT
