豆粑粑 guassian gjf2pdb
本帖最后由 meatball1982 于 2018-5-2 16:11 编辑Recently, have to convert gjf into pdb file.
Two ways,
01
newzmat.
02
gjf 2 xyz.
xyz 2pdb
A toy example.
wat.gjf
% nproc=8
% mem= 12GB
# mp2/6-31+G*
wat
0,1
O -0.00000 0.00000 6.84784
H -0.78400 0.00000 6.29384
H 0.78400 0.00000 6.29384
01. newzmat
newzmat -icart wat.gjf -opdb wat.pdbgaussian version should be higher than g09.D01
02.
a script convert gjf to xyz
We got a xyz file
./sh_gjf2xyz.sh wat.gjf3
0,1
O -0.00000 0.00000 6.84784
H -0.78400 0.00000 6.29384
H 0.78400 0.00000 6.29384
Then, with babel
babel -ixyz wat.xyz-opdb wat.pdb
a pdb file
COMPND 0,1
AUTHOR GENERATED BY OPEN BABEL 2.4.1
HETATM 1O HOH 1 0.000 0.000 6.8481.000.00 O
HETATM 2H HOH 0 -0.784 0.000 6.2941.000.00 H
HETATM 3H HOH 0 0.784 0.000 6.2941.000.00 H
CONECT 1 2 3
CONECT 2 1
CONECT 3 1
MASTER 0 0 0 0 0 0 0 0 3 0 3 0
END
If you got problem about the script, please feel free to contact me
meatball1982
meatball1982@163.com
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