[gmx-users] tfe
shahrbanoo karbalaee
shahrbanoo at gmail.com
Fri Aug 15 11:33:54 CEST 2008
Dear justin
I try again .but I get this error toputil .line 1364
not found such molecoule SOL.then would you please check my topol.top
file and advise me.
PEPTIDE A5 OR AUREIN 1.2
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_900 1 GLY N 1 -0.9 14.0067
; qtot -0.9
2 opls_909 1 GLY H1 1 0.36 1.008
; qtot -0.54
3 opls_909 1 GLY H2 1 0.36 1.008
; qtot -0.18
4 opls_906B 1 GLY CA 1 0.06 12.011
; qtot -0.12
5 opls_140 1 GLY HA1 1 0.06 1.008
; qtot -0.06
6 opls_140 1 GLY HA2 1 0.06 1.008 ; qtot 0
7 opls_235 1 GLY C 2 0.5 12.011 ; qtot 0.5
8 opls_236 1 GLY O 2 -0.5 15.9994 ; qtot 0
9 opls_238 2 LEU N 3 -0.5 14.0067
; qtot -0.5
10 opls_241 2 LEU H 3 0.3 1.008
; qtot -0.2
11 opls_224B 2 LEU CA 3 0.14 12.011
; qtot -0.06
12 opls_140 2 LEU HA 3 0.06 1.008 ; qtot 0
13 opls_136 2 LEU CB 4 -0.12 12.011
; qtot -0.12
14 opls_140 2 LEU HB1 4 0.06 1.008
; qtot -0.06
15 opls_140 2 LEU HB2 4 0.06 1.008 ; qtot 0
16 opls_137 2 LEU CG 5 -0.06 12.011
; qtot -0.06
17 opls_140 2 LEU HG 5 0.06 1.008 ; qtot 0
18 opls_135 2 LEU CD1 6 -0.18 12.011
; qtot -0.18
19 opls_140 2 LEU HD11 6 0.06 1.008
; qtot -0.12
20 opls_140 2 LEU HD12 6 0.06 1.008
; qtot -0.06
21 opls_140 2 LEU HD13 6 0.06 1.008 ; qtot 0
22 opls_135 2 LEU CD2 7 -0.18 12.011
; qtot -0.18
23 opls_140 2 LEU HD21 7 0.06 1.008
; qtot -0.12
24 opls_140 2 LEU HD22 7 0.06 1.008
; qtot -0.06
25 opls_140 2 LEU HD23 7 0.06 1.008 ; qtot 0
26 opls_235 2 LEU C 8 0.5 12.011 ; qtot 0.5
27 opls_236 2 LEU O 8 -0.5 15.9994 ; qtot 0
28 opls_238 3 PHE N 9 -0.5 14.0067
; qtot -0.5
29 opls_241 3 PHE H 9 0.3 1.008
; qtot -0.2
30 opls_224B 3 PHE CA 9 0.14 12.011
; qtot -0.06
31 opls_140 3 PHE HA 9 0.06 1.008 ; qtot 0
32 opls_149 3 PHE CB 10 -0.005 12.011
; qtot -0.005
33 opls_140 3 PHE HB1 10 0.06 1.008
; qtot 0.055
34 opls_140 3 PHE HB2 10 0.06 1.008
; qtot 0.115
35 opls_145 3 PHE CG 10 -0.115 12.011 ; qtot 0
36 opls_145 3 PHE CD1
219 opls_240 14 NH2 H2 73 0.38 1.008 ; qtot 0
[ bonds ]
[ pairs ]
[ angles ]
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3
4 9 7 8 1 improper_O_C_X_Y
7 11 9 10 1 improper_Z_N_X_Y
11 28 26 27 1 improper_O_C_X_Y
26 30 28 29 1 improper_Z_N_X_Y
30 48 46 47 1 improper_O_C_X_Y
32 35 38 36 1 improper_Z_CA_X_Y
35 40 36 37 1 improper_Z_CA_X_Y
35 42 38 39 1 improper_Z_CA_X_Y
36 44 40 41 1 improper_Z_CA_X_Y
38 44 42 43 1 improper_Z_CA_X_Y
40 42 44 45 1 improper_Z_CA_X_Y
46 50 48 49 1 improper_Z_N_X_Y
50 60 58 59 1 improper_O_C_X_Y
52 56 55 57 1 improper_O_C_X_Y
58 62 60 61 1 improper_Z_N_X_Y
62 79 77 78 1 improper_O_C_X_Y
77 81 79 80 1 improper_Z_N_X_Y
81 98 96 97 1 improper_O_C_X_Y
96 100 98 99 1 improper_Z_N_X_Y
100 120 118 119 1 improper_O_C_X_Y
118 122 120 121 1 improper_Z_N_X_Y
122 142 140 141 1 improper_O_C_X_Y
140 144 142 143 1 improper_Z_N_X_Y
144 161 159 160 1 improper_O_C_X_Y
159 163 161 162 1 improper_Z_N_X_Y
163 171 169 170 1 improper_O_C_X_Y
169 173 171 172 1 improper_Z_N_X_Y
173 186 184 185 1 improper_O_C_X_Y
178 182 181 183 1 improper_O_C_X_Y
184 188 186 187 1 improper_Z_N_X_Y
188 197 195 196 1 improper_O_C_X_Y
195 199 197 198 1 improper_Z_N_X_Y
199 217 215 216 1 improper_O_C_X_Y
201 204 207 205 1 improper_Z_CA_X_Y
204 209 205 206 1 improper_Z_CA_X_Y
204 211 207 208 1 improper_Z_CA_X_Y
205 213 209 210 1 improper_Z_CA_X_Y
207 213 211 212 1 improper_Z_CA_X_Y
209 211 213 214 1 improper_Z_CA_X_Y
215 218 217 219 1 improper_Z_N_X_Y
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
; Include water topology
#include "spce.itp"
Include tfe topology
#include "tfe.itp"
#endif
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
PEPTIDE A5 OR AUREIN 1.2 in 30%tfe water
[ molecules ]
; Compound #mols
Protein_A 1
SOL 941
tfe 301
---------------------------------------------------
and the file tfe.gro is:
Glycine aRginine prOline Methionine Alanine Cystine Serine
9
1TFE CC' 1 -0.098 -0.156 0.352
1TFE FD' 2 -0.010 -0.129 0.451
1TFE FE' 3 -0.143 -0.282 0.370
1TFE FF' 4 -0.203 -0.072 0.366
1TFE CB' 5 -0.033 -0.140 0.217
1TFE HB'1 6 -0.106 -0.161 0.139
1TFE HB'2 7 0.051 -0.209 0.209
1TFE O2' 8 0.014 -0.006 0.204
1TFE HO2 9 0.055 0.005 0.118
0.00000 0.00000 0.00000
thanks and best regards
--
sh-karbalaee
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