[gmx-users] what's wrong with my dummy atom definition?
吴显辉
nanyu101 at sina.com
Tue Nov 1 02:55:10 CET 2005
Dear gmx-users and Dr. Yang Ye
I need to create a cationic dummy atoms for my zinc enzyme. I just d=
o as Dr. Yang Ye and the mailing-list told. But the editconf and grompp d=
o not recognize my dummy atom when I create a box and a tpr file. At the =
beginning, I just run pdb2gmx to create a protein topology file without t=
he zinc cation. And then, I add the cationic dummy group to the end of gr=
o file produced by the pdb2gmx. After doing this, I try to create a box f=
or my whole system by editconf -bt cubic -f pro.gro -o pro_box.gro -p pro=
.top -c -d 1.0. In the pro_box.gro, the cationic dummy group was gone. Th=
e both gro file are listed here:
pro.gro (DZN is dummy group)
--------------------->
184ARG HD2 2879 3.932 1.483 3.431
184ARG NE 2880 3.834 1.338 3.332
184ARG HE 2881 3.747 1.380 3.360
184ARG CZ 2882 3.828 1.229 3.256
184ARG NH1 2883 3.940 1.169 3.217
184ARG HH11 2884 4.019 1.219 3.253
184ARG HH12 2885 3.917 1.090 3.161
184ARG NH2 2886 3.711 1.180 3.220
184ARG HH21 2887 3.637 1.236 3.258
184ARG HH22 2888 3.725 1.098 3.163
184ARG C 2889 4.340 1.577 3.248
184ARG O1 2890 4.428 1.679 3.229
184ARG O2 2891 4.344 1.456 3.187
185DZN DZ0 2893 17.682 8.854 32.262
185DZN DL1 2894 18.082 9.354 32.662
185DZN DL2 2895 17.682 8.854 33.162
185DZN DL3 2896 17.682 9.754 33.162
185DZN DL4 2897 18.582 8.854 33.162
<-----------------------------
the pro_box.gro (the dummy group does not exit)
------------------>
184ARG CD 2877 3.957 1.402 3.379
184ARG HD1 2878 4.004 1.337 3.439
184ARG HD2 2879 3.932 1.483 3.431
184ARG NE 2880 3.834 1.338 3.332
184ARG HE 2881 3.747 1.380 3.360
184ARG CZ 2882 3.828 1.229 3.256
184ARG NH1 2883 3.940 1.169 3.217
184ARG HH11 2884 4.019 1.219 3.253
184ARG HH12 2885 3.917 1.090 3.161
184ARG NH2 2886 3.711 1.180 3.220
184ARG HH21 2887 3.637 1.236 3.258
184ARG HH22 2888 3.725 1.098 3.163
184ARG C 2889 4.340 1.577 3.248
184ARG O1 2890 4.428 1.679 3.229
184ARG O2 2891 4.344 1.456 3.187
7.34890 7.34890 7.34890
<---------------------
Would you please give me some comments? Thank you very much.
My dummy atom type is listed here:
opls_966 DZ 65.37000 0.000 D 3.10000e-01 4.18200e-06
opls_967 DL 0.00000 0.500 D 0.00000e+00 0.00000e+00
And my itp file of dummy atoms is listed here.
------------------->
[ moleculetype ]
; molname nrexcl
dzn 2
; We use a strange order of atoms to make things go faster in GROMACS
[ atoms ]
; id at type res nr residu name at name cg nr charge
DZ0 opls_966 1 DZN DZ 1 0.000
DL1 opls_967 1 DZN DL 1 0.500
DL2 opls_967 1 DZN DL 1 0.500
DL3 opls_967 1 DZN DL 1 0.500
DL4 opls_967 1 DZN DL 1 0.500
[ bonds ]
DZ0 DL1
DZ0 DL2
DZ0 DL3
DZ0 DL4
[ constraints ]
; i j funct distance
1 2 1 0.090000
1 3 1 0.090000
1 4 1 0.090000
1 5 1 0.090000
[ exclusions ] =20
1 2 3 4 5
2 1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
[ dummies4 ] =20
; Dummy from funct a b d
5 1 2 3 4 1 0.33333 0.33333 -0.105
1 2 3 4 5 1 0.33333 0.33333 -0.105
2 3 4 5 1 1 0.33333 0.33333 -0.105
3 4 5 1 2 1 0.33333 0.33333 -0.105
4 5 1 2 4 1 0.33333 0.33333 -0.105
<---------------------
all your bests,
nanyu
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