I kept testing this procedure and now I am really confused. Running
antechamber to generate charges writes a few files to the directory:
ANTECHAMBER_AC.AC ANTECHAMBER_AM1BCC.AC ANTECHAMBER_BOND_TYPE.AC
ANTECHAMBER_PREP.AC ATOMTYPE.INF igp_gaff2.prepc igp.mol2 NEWPDB.PDB
sqm.in sqm.pdb
ANTECHAMBER_AC.AC0 ANTECHAMBER_AM1BCC_PRE.AC ANTECHAMBER_BOND_TYPE.AC0
ANTECHAMBER_PREP.AC0 igp1.prepc igp_gaff.prepc igp.prepc PREP.INF
sqm.out
If i keep them and run the command for gaff2 after gaff, I get the same
charges as the initial gaff run, however if I clear those files and run
antechamber again with -at gaff2, I get different charges.
Can somebody please help me with this, I don't understand why this is
happening, and I tried to google some information but I couldn't find
anything.
Also, where do I find information on what the atom types and bond types
mean, for example the ANTECHAMBER_BOND_TYPE.AC0 file atom and bond section.
What is O.co2 vs O.2, and for the bonds, what does 10 mean:
BOND 11 14 18 10 CE3 CZ3
BOND 12 14 12 10 CE3 CD2
BOND 13 18 19 10 CZ3 CH2
BOND 14 12 11 10 CD2 CG
BOND 15 12 13 10 CD2 CE2
BOND 16 11 15 10 CG CD1
BOND 17 19 17 10 CH2 CZ2
BOND 18 13 17 10 CE2 CZ2
BOND 19 13 16 10 CE2 NE1
BOND 20 15 16 10 CD1 NE1
I would really appreciate any help.
Thanks,
Yuliana
On Sat, Jul 28, 2018 at 3:31 PM, Yuliana Bosken <ydavi002.ucr.edu> wrote:
> 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
>
--
Yuliana Bosken
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Received on Sun Jul 29 2018 - 05:00:02 PDT
