[gmx-users] NADH topology
Keserű György dr.
gy.keseru at richter.hu
Wed Jun 9 10:59:45 CEST 2004
> Dear gmx-users,
> I would like to run a simulation with NADH using ffgmx. To do this I edited the corresponding pdb to match atom types listed in ffgmx.rtp and modify the residue name NADH in ffgmx.rtp to NAH. Consequently I used the residue name NAH in my pdb file. pdb2gmx successfully produced topology but grompp failed because of unknown proper torsion parameters.
> Would you please suggest a solution for this?
> Many thanks in advance,
>
> George
>
> PDB file:
>
> HEADER NAHH
> COMPND NAHH
> REMARK 08-JUN-04
> HETATM 3144 AP NAH A 1 -5.009 -5.237 9.697 1.00 0.00
> HETATM 3145 AO1P NAH A 1 -5.699 -6.329 10.406 1.00 0.00
> HETATM 3146 AO2P NAH A 1 -3.598 -4.934 9.997 1.00 0.00
> HETATM 3147 AO5* NAH A 1 -4.983 -5.720 8.188 1.00 0.00
> HETATM 3148 AC5* NAH A 1 -3.807 -6.329 7.649 1.00 0.00
> HETATM 3149 AC4* NAH A 1 -3.408 -7.613 8.408 1.00 0.00
> HETATM 3150 AO4* NAH A 1 -1.993 -7.674 8.447 1.00 0.00
> HETATM 3151 AC1* NAH A 1 -1.586 -8.424 7.323 1.00 0.00
> HETATM 3152 AC2* NAH A 1 -2.559 -9.598 7.355 1.00 0.00
> HETATM 3153 AC3* NAH A 1 -3.874 -8.907 7.705 1.00 0.00
> HETATM 3154 AO3* NAH A 1 -4.652 -9.769 8.522 1.00 0.00
> HETATM 3155 AH3* NAH A 1 -4.284 -9.780 9.439 1.00 0.00
> HETATM 3156 AO2* NAH A 1 -2.618 -10.327 6.137 1.00 0.00
> HETATM 3157 AH2* NAH A 1 -1.715 -10.348 5.752 1.00 0.00
> HETATM 3158 AN9 NAH A 1 -0.206 -8.906 7.464 1.00 0.00
> HETATM 3159 AC8 NAH A 1 0.686 -8.659 8.478 1.00 0.00
> HETATM 3160 AN7 NAH A 1 1.909 -9.056 8.231 1.00 0.00
> HETATM 3161 AC5 NAH A 1 1.800 -9.555 6.936 1.00 0.00
> HETATM 3162 AC6 NAH A 1 2.749 -9.957 5.993 1.00 0.00
> HETATM 3163 AN6 NAH A 1 4.043 -9.849 6.253 1.00 0.00
> HETATM 3164 AH61 NAH A 1 4.736 -10.219 5.607 1.00 0.00
> HETATM 3165 AH62 NAH A 1 4.286 -9.677 7.218 1.00 0.00
> HETATM 3166 AN1 NAH A 1 2.349 -10.385 4.793 1.00 0.00
> HETATM 3167 AC2 NAH A 1 1.044 -10.457 4.548 1.00 0.00
> HETATM 3168 AN3 NAH A 1 0.038 -10.087 5.337 1.00 0.00
> HETATM 3169 AC4 NAH A 1 0.507 -9.568 6.501 1.00 0.00
> HETATM 3170 O3P NAH A 1 -5.901 -3.912 9.569 1.00 0.00
> HETATM 3171 NP NAH A 1 -6.332 -3.095 10.877 1.00 0.00
> HETATM 3172 NO1P NAH A 1 -5.163 -2.598 11.627 1.00 0.00
> HETATM 3173 NO2P NAH A 1 -7.375 -3.838 11.595 1.00 0.00
> HETATM 3174 NO5* NAH A 1 -7.091 -1.820 10.292 1.00 0.00
> HETATM 3175 NC5* NAH A 1 -6.528 -0.507 10.415 1.00 0.00
> HETATM 3176 NC4* NAH A 1 -5.805 -0.065 9.138 1.00 0.00
> HETATM 3177 NO4* NAH A 1 -4.911 -1.083 8.676 1.00 0.00
> HETATM 3178 NC1* NAH A 1 -5.456 -1.688 7.506 1.00 0.00
> HETATM 3179 NC2* NAH A 1 -6.821 -1.039 7.219 1.00 0.00
> HETATM 3180 NC3* NAH A 1 -6.800 0.259 8.012 1.00 0.00
> HETATM 3181 NO3* NAH A 1 -6.332 1.253 7.116 1.00 0.00
> HETATM 3182 NH3* NAH A 1 -7.112 1.760 6.782 1.00 0.00
> HETATM 3183 NO2* NAH A 1 -7.015 -0.712 5.862 1.00 0.00
> HETATM 3184 NH2* NAH A 1 -6.468 0.086 5.765 1.00 0.00
> HETATM 3185 NN1 NAH A 1 -4.448 -1.579 6.411 1.00 0.00
> HETATM 3186 NC2 NAH A 1 -3.779 -2.734 5.967 1.00 0.00
> HETATM 3187 NC3 NAH A 1 -2.696 -2.745 5.061 1.00 0.00
> HETATM 3188 NC7 NAH A 1 -1.997 -4.018 4.779 1.00 0.00
> HETATM 3189 NO7 NAH A 1 -2.244 -5.018 5.450 1.00 0.00
> HETATM 3190 NN7 NAH A 1 -1.088 -4.094 3.834 1.00 0.00>
> HETATM 3191 NH71 NAH A 1 -0.915 -3.306 3.240 1.00 0.00
> HETATM 3192 NH72 NAH A 1 -0.606 -4.970 3.656 1.00 0.00
> HETATM 3193 NC4 NAH A 1 -2.235 -1.458 4.408 1.00 0.00
> HETATM 3194 NC5 NAH A 1 -2.766 -0.262 5.178 1.00 0.00
> HETATM 3195 NC6 NAH A 1 -3.795 -0.369 6.129 1.00 0.00
> CONECT 3144 3145 3146 3147 3170
> CONECT 3145 3144
> CONECT 3146 3144
> CONECT 3147 3144 3148
> CONECT 3148 3147 3149
> CONECT 3149 3148 3150 3153
> CONECT 3150 3149 3151
> CONECT 3151 3150 3152
> CONECT 3152 3151 3153 3156
> CONECT 3153 3149 3152 3154
> CONECT 3154 3153 3155
> CONECT 3155 3154
> CONECT 3156 3152 3157
> CONECT 3157 3156
> CONECT 3158 3159 3169
> CONECT 3159 3158 3160
> CONECT 3160 3159 3161
> CONECT 3161 3160 3162 3169
> CONECT 3162 3161 3163 3166
> CONECT 3163 3162 3164 3165
> CONECT 3164 3163
> CONECT 3165 3163
> CONECT 3166 3162 3167
> CONECT 3167 3166 3168
> CONECT 3168 3167 3169
> CONECT 3169 3158 3161 3168
> CONECT 3170 3144 3171
> CONECT 3171 3170 3172 3173 3174
> CONECT 3172 3171
> CONECT 3173 3171
> CONECT 3174 3171 3175
> CONECT 3175 3174 3176
> CONECT 3176 3175 3177 3180
> CONECT 3177 3176 3178
> CONECT 3178 3177 3179 3185
> CONECT 3179 3178 3180 3183
> CONECT 3180 3176 3179 3181
> CONECT 3181 3180 3182
> CONECT 3182 3181
> CONECT 3183 3179 3184
> CONECT 3184 3183
> CONECT 3185 3178 3186 3195
> CONECT 3186 3185 3187 >
> CONECT 3187 3186 3188 3193
> CONECT 3188 3187 3189 3190
> CONECT 3189 3188
> CONECT 3190 3188 3191 3192
> CONECT 3191 3190
> CONECT 3192 3190
> CONECT 3193 3187 3194
> CONECT 3194 3193 3195
> CONECT 3195 3185 3194
> CONECT 3196 3197
> CONECT 3197 3196
> END
>
> After pdb2gmx produced topology I run grompp using the following command and got this error
>
> [keseru at clusterserver nor]$ grompp_mpi -v -f em.mdp -c nadh.gro -o nadh_em.tpr -
> p nadh.top
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> WARNING 1 [file "nadh.top", line 312]:
> No default Proper Dih. types, using zeroes
> WARNING 2 [file "nadh.top", line 313]:
> No default Proper Dih. types, using zeroes
> WARNING 3 [file "nadh.top", line 315]:
> No default Proper Dih. types, using zeroes
> WARNING 4 [file "nadh.top", line 316]:
> No default Proper Dih. types, using zeroes
> WARNING 5 [file "nadh.top", line 318]:
> No default Proper Dih. types, using zeroes
> WARNING 6 [file "nadh.top", line 320]:
> No default Proper Dih. types, using zeroes
> WARNING 7 [file "nadh.top", line 323]:
> No default Proper Dih. types, using zeroes
> WARNING 8 [file "nadh.top", line 326]:
> No default Proper Dih. types, using zeroes
> WARNING 9 [file "nadh.top", line 328]:
> No default Proper Dih. types, using zeroes
> WARNING 10 [file "nadh.top", line 330]:
> No default Proper Dih. types, using zeroes
> Cleaning up temporary file gromppWUjJAW
> Fatal error: Too many warnings, grompp_mpi terminated
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