The AWK command is space sensitive, it looks like that at least one space wasn't copied adequately. You want to make sure your PDB is respecting the following format naming convention: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
> On 11 Jan 2016, at 23:50, Bin Wang <ben.wangbj.gmail.com> wrote:
>
> Dear Jean-Marc and Bill,
>
> Thank you so much for the help!
> I ran that awk program, and changed the residue numbers for all PA and PS.
> It didn't work on WAT and K+, so I just deleted all of the water molecules,
> and added TER between each K+ ion. When I try to load this pdb file into
> xleap, it shows errors like these:
>
>> p = loadpdb prp-membrane_awk_nowater.pdb
> Loading PDB file: ./prp-membrane_awk_nowater.pdb
> Enter zPdbReadScan from call depth 0.
> -- residue 2560: duplicate [ HN1] atoms (total 3)
> -- residue 2561: duplicate [ C11] atoms (total 9)
> -- residue 2561: duplicate [ H11] atoms (total 2)
> -- residue 2561: duplicate [ H12] atoms (total 2)
> -- residue 2561: duplicate [ H13] atoms (total 2)
> -- residue 2561: duplicate [ H14] atoms (total 2)
> -- residue 2561: duplicate [ H15] atoms (total 2)
> -- residue 2561: duplicate [ H16] atoms (total 2)
> -- residue 2561: duplicate [ H17] atoms (total 2)
> -- residue 2561: duplicate [ H18] atoms (total 3)
> -- residue 2562: duplicate [ C11] atoms (total 7)
> -- residue 2562: duplicate [ H10] atoms (total 2)
> -- residue 2562: duplicate [ H11] atoms (total 2)
> -- residue 2562: duplicate [ H12] atoms (total 2)
> -- residue 2562: duplicate [ H13] atoms (total 2)
> -- residue 2562: duplicate [ H14] atoms (total 2)
> -- residue 2562: duplicate [ H15] atoms (total 2)
> -- residue 2562: duplicate [ H16] atoms (total 3)
> -- residue 2563: duplicate [ HN1] atoms (total 3)
> -- residue 2564: duplicate [ C11] atoms (total 9)
> ......
>
> Then the xleap automatically shut down.
>
>
>
>
>
> On Mon, Jan 11, 2016 at 3:17 PM, JEAN MARC BILLOD <jmbillod.cib.csic.es>
> wrote:
>
>> In order to do the renaming of the whole PDB in an automated way you
>> can try to use this AWK script in a terminal (by replacing INPUT by
>> the name of your PDB present in the current folder and OUTPUT by the
>> name you want):
>>
>> awk 'BEGIN{a=0;b=0;c=0}{if($1=="TER"||(((b!=$4 &&
>> $1!="TER")||($3=="N")||($4=="WAT" &&
>> $3=="O")||($3=="Cl-")||($3=="K+")) &&
>> c==0)){x++};if($1!="TER"){c=0;b=$4;a++;printf "%-6s%5d %-4s%1s%-3s
>> %1s%4d%1s %8.3f%8.3f%8.3f%6.2f%6.2f %-4s%2s%2s\n",$1,a,$3,"
>> ",$4," ",x," ",$6,$7,$8,"","",$NF," "," "}else{c=1;print $0}}' INPUT >
>> OUTPUT
>>
>> The command doesn't work in every situation, it might require some
>> modifications, hopefully it will work as it is in your case.
>> Good luck,
>> Jean-Marc
>>
>> Quoting Bill Ross <ross.cgl.ucsf.edu>:
>>
>>> Try numbering your residues consecutively in your pdb file:
>>>
>>> ATOM 3212 H16R PA 1 -28.039 -6.444 -1.295 1.00 0.00
>> MEMB
>>> ATOM 3213 H16S PA 1 -27.329 -7.017 -2.902 1.00 0.00
>> MEMB
>>> ATOM 3214 H16T PA 1 -27.656 -5.257 -2.520 1.00 0.00
>> MEMB
>>> ATOM 3081 N31 PC 1 -23.308 -3.619 18.178 1.00 0.00
>> MEMB
>>> ATOM 3082 C32 PC 1 -24.638 -3.889 18.878 1.00 0.00
>> MEMB
>>>
>>> E.g. start at 1 and go up. Here PA and PC are both residue 1.
>>>
>>> Bill
>>>
>>>> On 1/11/16 7:40 AM, Bin Wang wrote:
>>>> Hello Jean-Marc,
>>>>
>>>> The pdb file is too big, I am not sure if it can pass the moderator
>>>> approval, but I can show some of it here.
>>>>
>>>> ATOM 3069 N SER 209 1.510 -13.265 27.057 1.00 0.00
>> PROA
>>>> ATOM 3070 HN SER 209 1.024 -13.347 27.923 1.00 0.00
>> PROA
>>>> ATOM 3071 CA SER 209 2.846 -13.823 27.050 1.00 0.00
>> PROA
>>>> ATOM 3072 HA SER 209 3.297 -13.607 26.093 1.00 0.00
>> PROA
>>>> ATOM 3073 CB SER 209 3.697 -13.194 28.213 1.00 0.00
>> PROA
>>>> ATOM 3074 HB1 SER 209 4.744 -13.562 28.186 1.00 0.00
>> PROA
>>>> ATOM 3075 HB2 SER 209 3.249 -13.421 29.204 1.00 0.00
>> PROA
>>>> ATOM 3076 OG SER 209 3.660 -11.774 27.962 1.00 0.00
>> PROA
>>>> ATOM 3077 HG1 SER 209 2.820 -11.604 27.528 1.00 0.00
>> PROA
>>>> ATOM 3078 C SER 209 2.929 -15.385 27.067 1.00 0.00
>> PROA
>>>> ATOM 3079 OT1 SER 209 1.849 -16.034 27.085 1.00 0.00
>> PROA
>>>> ATOM 3080 OT2 SER 209 4.071 -15.917 27.062 1.00 0.00
>> PROA
>>>> TER
>>>> ATOM 3122 C12 PA 1 -24.586 -8.150 11.577 1.00 0.00
>> MEMB
>>>> ATOM 3123 H2R PA 1 -23.489 -8.319 11.531 1.00 0.00
>> MEMB
>>>> ATOM 3124 H2S PA 1 -24.774 -7.205 11.024 1.00 0.00
>> MEMB
>>>> ATOM 3172 C13 PA 1 -25.136 -9.331 10.737 1.00 0.00
>> MEMB
>>>> ATOM 3173 H3R PA 1 -26.199 -9.166 10.459 1.00 0.00
>> MEMB
>>>> ATOM 3174 H3S PA 1 -25.072 -10.310 11.259 1.00 0.00
>> MEMB
>>>> ATOM 3175 C14 PA 1 -24.307 -9.647 9.516 1.00 0.00
>> MEMB
>>>> ATOM 3176 H4R PA 1 -24.627 -10.591 9.027 1.00 0.00
>> MEMB
>>>> ATOM 3177 H4S PA 1 -23.257 -9.911 9.765 1.00 0.00
>> MEMB
>>>> ATOM 3178 C15 PA 1 -24.245 -8.525 8.489 1.00 0.00
>> MEMB
>>>> ATOM 3179 H5R PA 1 -23.748 -7.681 9.014 1.00 0.00
>> MEMB
>>>> ATOM 3180 H5S PA 1 -25.276 -8.212 8.217 1.00 0.00
>> MEMB
>>>> ATOM 3181 C16 PA 1 -23.618 -8.997 7.203 1.00 0.00
>> MEMB
>>>> ATOM 3182 H6R PA 1 -24.247 -9.867 6.917 1.00 0.00
>> MEMB
>>>> ATOM 3183 H6S PA 1 -22.571 -9.290 7.431 1.00 0.00
>> MEMB
>>>> ATOM 3184 C17 PA 1 -23.730 -8.022 5.955 1.00 0.00
>> MEMB
>>>> ATOM 3185 H7R PA 1 -23.297 -7.029 6.204 1.00 0.00
>> MEMB
>>>> ATOM 3186 H7S PA 1 -24.817 -7.842 5.814 1.00 0.00
>> MEMB
>>>> ATOM 3187 C18 PA 1 -23.103 -8.612 4.653 1.00 0.00
>> MEMB
>>>> ATOM 3188 H8R PA 1 -22.053 -8.927 4.836 1.00 0.00
>> MEMB
>>>> ATOM 3189 H8S PA 1 -23.026 -7.797 3.903 1.00 0.00
>> MEMB
>>>> ATOM 3190 C19 PA 1 -23.819 -9.772 4.016 1.00 0.00
>> MEMB
>>>> ATOM 3191 H9R PA 1 -24.922 -9.756 4.147 1.00 0.00
>> MEMB
>>>> ATOM 3192 H9S PA 1 -23.480 -10.701 4.523 1.00 0.00
>> MEMB
>>>> ATOM 3193 C110 PA 1 -23.466 -10.112 2.495 1.00 0.00
>> MEMB
>>>> ATOM 3194 H10R PA 1 -23.846 -11.150 2.376 1.00 0.00
>> MEMB
>>>> ATOM 3195 H10S PA 1 -22.368 -10.018 2.355 1.00 0.00
>> MEMB
>>>> ATOM 3196 C111 PA 1 -24.156 -9.078 1.498 1.00 0.00
>> MEMB
>>>> ATOM 3197 H11R PA 1 -23.901 -9.333 0.447 1.00 0.00
>> MEMB
>>>> ATOM 3198 H11S PA 1 -23.584 -8.157 1.741 1.00 0.00
>> MEMB
>>>> ATOM 3199 C112 PA 1 -25.627 -8.697 1.584 1.00 0.00
>> MEMB
>>>> ATOM 3200 H12R PA 1 -25.875 -8.473 2.644 1.00 0.00
>> MEMB
>>>> ATOM 3201 H12S PA 1 -26.232 -9.574 1.270 1.00 0.00
>> MEMB
>>>> ATOM 3202 C113 PA 1 -25.986 -7.420 0.783 1.00 0.00
>> MEMB
>>>> ATOM 3203 H13R PA 1 -25.488 -6.585 1.319 1.00 0.00
>> MEMB
>>>> ATOM 3204 H13S PA 1 -27.087 -7.272 0.812 1.00 0.00
>> MEMB
>>>> ATOM 3205 C114 PA 1 -25.491 -7.448 -0.710 1.00 0.00
>> MEMB
>>>> ATOM 3206 H14R PA 1 -25.987 -8.339 -1.153 1.00 0.00
>> MEMB
>>>> ATOM 3207 H14S PA 1 -24.385 -7.545 -0.680 1.00 0.00
>> MEMB
>>>> ATOM 3208 C115 PA 1 -25.925 -6.117 -1.358 1.00 0.00
>> MEMB
>>>> ATOM 3209 H15R PA 1 -25.096 -5.748 -1.999 1.00 0.00
>> MEMB
>>>> ATOM 3210 H15S PA 1 -26.066 -5.248 -0.680 1.00 0.00
>> MEMB
>>>> ATOM 3211 C116 PA 1 -27.318 -6.235 -2.113 1.00 0.00
>> MEMB
>>>> ATOM 3212 H16R PA 1 -28.039 -6.444 -1.295 1.00 0.00
>> MEMB
>>>> ATOM 3213 H16S PA 1 -27.329 -7.017 -2.902 1.00 0.00
>> MEMB
>>>> ATOM 3214 H16T PA 1 -27.656 -5.257 -2.520 1.00 0.00
>> MEMB
>>>> ATOM 3081 N31 PC 1 -23.308 -3.619 18.178 1.00 0.00
>> MEMB
>>>> ATOM 3082 C32 PC 1 -24.638 -3.889 18.878 1.00 0.00
>> MEMB
>>>> ATOM 3083 H2A PC 1 -25.456 -3.445 18.329 1.00 0.00
>> MEMB
>>>> ATOM 3084 H2B PC 1 -24.624 -3.338 19.807 1.00 0.00
>> MEMB
>>>> ATOM 3085 C33 PC 1 -22.223 -3.886 19.200 1.00 0.00
>> MEMB
>>>> ATOM 3086 H3A PC 1 -22.331 -3.337 20.123 1.00 0.00
>> MEMB
>>>> ATOM 3087 H3B PC 1 -22.248 -4.920 19.513 1.00 0.00
>> MEMB
>>>> ATOM 3088 H3C PC 1 -21.233 -3.686 18.819 1.00 0.00
>> MEMB
>>>> ATOM 3089 C34 PC 1 -23.227 -4.441 16.900 1.00 0.00
>> MEMB
>>>> ATOM 3090 H4A PC 1 -22.478 -3.894 16.347 1.00 0.00
>> MEMB
>>>> ATOM 3091 H4B PC 1 -23.007 -5.454 17.203 1.00 0.00
>> MEMB
>>>> ATOM 3092 H4C PC 1 -24.187 -4.331 16.416 1.00 0.00
>> MEMB
>>>> ATOM 3093 C35 PC 1 -23.171 -2.137 17.716 1.00 0.00
>> MEMB
>>>> ATOM 3094 H5A PC 1 -23.377 -1.506 18.568 1.00 0.00
>> MEMB
>>>> ATOM 3095 H5B PC 1 -23.839 -1.922 16.895 1.00 0.00
>> MEMB
>>>> ATOM 3096 H5C PC 1 -22.170 -1.893 17.392 1.00 0.00
>> MEMB
>>>> ATOM 3097 C31 PC 1 -25.092 -5.330 19.211 1.00 0.00
>> MEMB
>>>> ATOM 3098 H1A PC 1 -25.159 -5.912 18.267 1.00 0.00
>> MEMB
>>>> ATOM 3099 H1B PC 1 -26.089 -5.335 19.701 1.00 0.00
>> MEMB
>>>> ATOM 3100 P31 PC 1 -23.432 -7.226 19.811 1.00 0.00
>> MEMB
>>>> ATOM 3101 O33 PC 1 -24.333 -8.282 20.419 1.00 0.00
>> MEMB
>>>> ATOM 3102 O34 PC 1 -21.985 -7.286 20.285 1.00 0.00
>> MEMB
>>>> ATOM 3103 O32 PC 1 -24.124 -5.843 20.135 1.00 0.00
>> MEMB
>>>> ATOM 3104 O31 PC 1 -23.418 -7.426 18.267 1.00 0.00
>> MEMB
>>>> ATOM 3105 C3 PC 1 -23.938 -8.548 17.597 1.00 0.00
>> MEMB
>>>> ATOM 3106 HA PC 1 -25.043 -8.620 17.499 1.00 0.00
>> MEMB
>>>> ATOM 3107 HB PC 1 -23.671 -9.532 18.039 1.00 0.00
>> MEMB
>>>> ATOM 3108 C2 PC 1 -23.426 -8.530 16.082 1.00 0.00
>> MEMB
>>>> ATOM 3109 HX PC 1 -23.301 -9.551 15.661 1.00 0.00
>> MEMB
>>>> ATOM 3110 O21 PC 1 -22.321 -7.737 15.905 1.00 0.00
>> MEMB
>>>> ATOM 3111 C21 PC 1 -21.231 -8.211 16.337 1.00 0.00
>> MEMB
>>>> ATOM 3112 O22 PC 1 -21.117 -9.252 16.942 1.00 0.00
>> MEMB
>>>> ATOM 3116 C1 PC 1 -24.589 -7.895 15.251 1.00 0.00
>> MEMB
>>>> ATOM 3117 HR PC 1 -24.890 -6.881 15.591 1.00 0.00
>> MEMB
>>>> ATOM 3118 HS PC 1 -25.520 -8.472 15.437 1.00 0.00
>> MEMB
>>>> ATOM 3119 O11 PC 1 -24.208 -7.880 13.867 1.00 0.00
>> MEMB
>>>> ATOM 3120 C11 PC 1 -25.175 -8.100 12.940 1.00 0.00
>> MEMB
>>>> ATOM 3121 O12 PC 1 -26.327 -8.196 13.211 1.00 0.00
>> MEMB
>>>> ATOM 3113 C12 OL 1 -20.204 -7.395 15.660 1.00 0.00
>> MEMB
>>>> ATOM 3114 H2R OL 1 -19.222 -7.421 16.179 1.00 0.00
>> MEMB
>>>> ATOM 3115 H2S OL 1 -20.487 -6.339 15.464 1.00 0.00
>> MEMB
>>>> ATOM 3125 C13 OL 1 -20.074 -7.911 14.209 1.00 0.00
>> MEMB
>>>> ATOM 3126 H3R OL 1 -20.356 -8.985 14.193 1.00 0.00
>> MEMB
>>>> ATOM 3127 H3S OL 1 -18.987 -7.835 13.993 1.00 0.00
>> MEMB
>>>> ATOM 3128 C14 OL 1 -20.774 -6.897 13.180 1.00 0.00
>> MEMB
>>>> ATOM 3129 H4R OL 1 -20.167 -5.971 13.274 1.00 0.00
>> MEMB
>>>> ATOM 3130 H4S OL 1 -21.854 -6.665 13.296 1.00 0.00
>> MEMB
>>>> ATOM 3131 C15 OL 1 -20.574 -7.422 11.773 1.00 0.00
>> MEMB
>>>> ATOM 3132 H5R OL 1 -20.942 -8.454 11.590 1.00 0.00
>> MEMB
>>>> ATOM 3133 H5S OL 1 -19.475 -7.432 11.617 1.00 0.00
>> MEMB
>>>> ATOM 3134 C16 OL 1 -21.178 -6.656 10.685 1.00 0.00
>> MEMB
>>>> ATOM 3135 H6R OL 1 -20.842 -5.597 10.702 1.00 0.00
>> MEMB
>>>> ATOM 3136 H6S OL 1 -22.272 -6.797 10.820 1.00 0.00
>> MEMB
>>>> ATOM 3137 C17 OL 1 -20.782 -7.149 9.224 1.00 0.00
>> MEMB
>>>> ATOM 3138 H7R OL 1 -21.430 -6.432 8.676 1.00 0.00
>> MEMB
>>>> ATOM 3139 H7S OL 1 -21.181 -8.148 8.948 1.00 0.00
>> MEMB
>>>> ATOM 3140 C18 OL 1 -19.294 -7.073 8.899 1.00 0.00
>> MEMB
>>>> ATOM 3141 H8R OL 1 -19.156 -7.407 7.849 1.00 0.00
>> MEMB
>>>> ATOM 3142 H8S OL 1 -18.699 -7.802 9.490 1.00 0.00
>> MEMB
>>>> ATOM 3143 C19 OL 1 -18.573 -5.763 9.059 1.00 0.00
>> MEMB
>>>> ATOM 3144 H9R OL 1 -18.598 -5.331 10.071 1.00 0.00
>> MEMB
>>>> ATOM 3145 C110 OL 1 -18.025 -4.998 8.153 1.00 0.00
>> MEMB
>>>> ATOM 3146 H10R OL 1 -17.642 -4.080 8.622 1.00 0.00
>> MEMB
>>>> ATOM 3147 C111 OL 1 -18.025 -5.256 6.686 1.00 0.00
>> MEMB
>>>> ATOM 3148 H11R OL 1 -18.010 -6.348 6.484 1.00 0.00
>> MEMB
>>>> ATOM 3149 H11S OL 1 -17.071 -4.875 6.264 1.00 0.00
>> MEMB
>>>> ATOM 3150 C112 OL 1 -19.192 -4.678 5.899 1.00 0.00
>> MEMB
>>>> ATOM 3151 H12R OL 1 -19.119 -3.569 5.907 1.00 0.00
>> MEMB
>>>> ATOM 3152 H12S OL 1 -20.209 -5.030 6.172 1.00 0.00
>> MEMB
>>>> ATOM 3153 C113 OL 1 -19.257 -5.071 4.321 1.00 0.00
>> MEMB
>>>> ATOM 3154 H13R OL 1 -19.273 -6.177 4.226 1.00 0.00
>> MEMB
>>>> ATOM 3155 H13S OL 1 -18.332 -4.656 3.866 1.00 0.00
>> MEMB
>>>> ATOM 3156 C114 OL 1 -20.622 -4.491 3.881 1.00 0.00
>> MEMB
>>>> ATOM 3157 H14R OL 1 -20.630 -3.400 4.093 1.00 0.00
>> MEMB
>>>> ATOM 3158 H14S OL 1 -21.442 -4.864 4.530 1.00 0.00
>> MEMB
>>>> ATOM 3159 C115 OL 1 -20.854 -4.852 2.394 1.00 0.00
>> MEMB
>>>> ATOM 3160 H15R OL 1 -20.230 -5.753 2.218 1.00 0.00
>> MEMB
>>>> ATOM 3161 H15S OL 1 -20.634 -4.004 1.711 1.00 0.00
>> MEMB
>>>> ATOM 3162 C116 OL 1 -22.326 -5.132 2.117 1.00 0.00
>> MEMB
>>>> ATOM 3163 H16R OL 1 -22.582 -5.953 2.821 1.00 0.00
>> MEMB
>>>> ATOM 3164 H16S OL 1 -22.496 -5.443 1.064 1.00 0.00
>> MEMB
>>>> ATOM 3165 C117 OL 1 -23.283 -3.892 2.328 1.00 0.00
>> MEMB
>>>> ATOM 3166 H17R OL 1 -22.974 -3.441 3.295 1.00 0.00
>> MEMB
>>>> ATOM 3167 H17S OL 1 -24.333 -4.253 2.327 1.00 0.00
>> MEMB
>>>> ATOM 3168 C118 OL 1 -23.094 -2.765 1.284 1.00 0.00
>> MEMB
>>>> ATOM 3169 H18R OL 1 -23.687 -1.888 1.622 1.00 0.00
>> MEMB
>>>> ATOM 3170 H18S OL 1 -23.518 -3.065 0.302 1.00 0.00
>> MEMB
>>>> ATOM 3171 H18T OL 1 -22.018 -2.532 1.133 1.00 0.00
>> MEMB
>>>> TER
>>>> ATOM 3256 C12 PA 2 -23.647 13.219 12.610 1.00 0.00
>> MEMB
>>>> ATOM 3257 H2R PA 2 -24.655 12.962 12.219 1.00 0.00
>> MEMB
>>>> ATOM 3258 H2S PA 2 -23.121 12.255 12.777 1.00 0.00
>> MEMB
>>>> ATOM 3306 C13 PA 2 -22.829 14.079 11.593 1.00 0.00
>> MEMB
>>>> ATOM 3307 H3R PA 2 -21.913 14.518 12.043 1.00 0.00
>> MEMB
>>>> ATOM 3308 H3S PA 2 -23.424 14.952 11.251 1.00 0.00
>> MEMB
>>>> ATOM 3309 C14 PA 2 -22.350 13.296 10.326 1.00 0.00
>> MEMB
>>>> ATOM 3310 H4R PA 2 -22.133 14.083 9.573 1.00 0.00
>> MEMB
>>>> ATOM 3311 H4S PA 2 -23.288 12.893 9.888 1.00 0.00
>> MEMB
>>>> ......
>>>> ATOM ***** H18S OL 799 85.960 64.387 -0.059 1.00 0.00
>> MEMB
>>>> ATOM ***** H18T OL 799 84.140 64.328 -0.002 1.00 0.00
>> MEMB
>>>> TER
>>>> ATOM ***** C12 PA 800 79.753 83.954 -11.958 1.00 0.00
>> MEMB
>>>> ATOM ***** H2R PA 800 78.646 84.053 -11.985 1.00 0.00
>> MEMB
>>>> ATOM ***** H2S PA 800 80.303 84.704 -12.566 1.00 0.00
>> MEMB
>>>> ATOM ***** C13 PA 800 80.304 84.251 -10.590 1.00 0.00
>> MEMB
>>>> ATOM ***** H3R PA 800 80.567 85.327 -10.508 1.00 0.00
>> MEMB
>>>> ATOM ***** H3S PA 800 81.317 83.803 -10.508 1.00 0.00
>> MEMB
>>>> ATOM ***** C14 PA 800 79.403 83.926 -9.401 1.00 0.00
>> MEMB
>>>> ATOM ***** H4R PA 800 79.489 82.866 -9.078 1.00 0.00
>> MEMB
>>>> ATOM ***** H4S PA 800 78.397 84.025 -9.863 1.00 0.00
>> MEMB
>>>> ATOM ***** C15 PA 800 79.509 84.891 -8.221 1.00 0.00
>> MEMB
>>>> ATOM ***** H5R PA 800 79.357 85.930 -8.585 1.00 0.00
>> MEMB
>>>> ATOM ***** H5S PA 800 80.518 84.736 -7.783 1.00 0.00
>> MEMB
>>>> ATOM ***** C16 PA 800 78.474 84.665 -7.093 1.00 0.00
>> MEMB
>>>> ATOM ***** H6R PA 800 77.441 84.970 -7.366 1.00 0.00
>> MEMB
>>>> ATOM ***** H6S PA 800 78.699 85.451 -6.341 1.00 0.00
>> MEMB
>>>> ATOM ***** C17 PA 800 78.389 83.306 -6.503 1.00 0.00
>> MEMB
>>>> ATOM ***** H7R PA 800 77.974 82.568 -7.223 1.00 0.00
>> MEMB
>>>> ATOM ***** H7S PA 800 77.597 83.417 -5.732 1.00 0.00
>> MEMB
>>>> ATOM ***** C18 PA 800 79.667 82.760 -5.925 1.00 0.00
>> MEMB
>>>> ATOM ***** H8R PA 800 79.410 82.522 -4.871 1.00 0.00
>> MEMB
>>>> ATOM ***** H8S PA 800 80.494 83.500 -5.994 1.00 0.00
>> MEMB
>>>> ATOM ***** C19 PA 800 80.237 81.489 -6.498 1.00 0.00
>> MEMB
>>>> ATOM ***** H9R PA 800 80.549 81.656 -7.551 1.00 0.00
>> MEMB
>>>> ATOM ***** H9S PA 800 79.466 80.696 -6.387 1.00 0.00
>> MEMB
>>>> ATOM ***** C110 PA 800 81.508 80.880 -5.856 1.00 0.00
>> MEMB
>>>> ATOM ***** H10R PA 800 82.257 81.676 -6.053 1.00 0.00
>> MEMB
>>>> ATOM ***** H10S PA 800 81.778 79.945 -6.392 1.00 0.00
>> MEMB
>>>> ATOM ***** C111 PA 800 81.439 80.602 -4.320 1.00 0.00
>> MEMB
>>>> ATOM ***** H11R PA 800 81.307 81.601 -3.851 1.00 0.00
>> MEMB
>>>> ATOM ***** H11S PA 800 82.459 80.263 -4.042 1.00 0.00
>> MEMB
>>>> ATOM ***** C112 PA 800 80.402 79.571 -3.944 1.00 0.00
>> MEMB
>>>> ATOM ***** H12R PA 800 80.651 78.621 -4.463 1.00 0.00
>> MEMB
>>>> ATOM ***** H12S PA 800 79.378 79.822 -4.293 1.00 0.00
>> MEMB
>>>> ATOM ***** C113 PA 800 80.515 79.295 -2.362 1.00 0.00
>> MEMB
>>>> ATOM ***** H13R PA 800 81.469 79.753 -2.023 1.00 0.00
>> MEMB
>>>> ATOM ***** H13S PA 800 80.543 78.203 -2.161 1.00 0.00
>> MEMB
>>>> ATOM ***** C114 PA 800 79.555 80.228 -1.580 1.00 0.00
>> MEMB
>>>> ATOM ***** H14R PA 800 78.518 80.055 -1.938 1.00 0.00
>> MEMB
>>>> ATOM ***** H14S PA 800 79.881 81.246 -1.882 1.00 0.00
>> MEMB
>>>> ATOM ***** C115 PA 800 79.639 80.043 -0.045 1.00 0.00
>> MEMB
>>>> ATOM ***** H15R PA 800 80.694 80.064 0.303 1.00 0.00
>> MEMB
>>>> ATOM ***** H15S PA 800 79.244 79.018 0.122 1.00 0.00
>> MEMB
>>>> ATOM ***** C116 PA 800 78.642 81.027 0.533 1.00 0.00
>> MEMB
>>>> ATOM ***** H16R PA 800 77.646 80.543 0.437 1.00 0.00
>> MEMB
>>>> ATOM ***** H16S PA 800 78.622 81.989 -0.022 1.00 0.00
>> MEMB
>>>> ATOM ***** H16T PA 800 78.793 81.233 1.615 1.00 0.00
>> MEMB
>>>> ATOM ***** N31 PS 800 74.635 82.772 -20.229 1.00 0.00
>> MEMB
>>>> ATOM ***** HN1A PS 800 74.665 83.393 -19.395 1.00 0.00
>> MEMB
>>>> ATOM ***** HN1B PS 800 75.145 83.113 -21.069 1.00 0.00
>> MEMB
>>>> ATOM ***** HN1C PS 800 73.647 82.680 -20.541 1.00 0.00
>> MEMB
>>>> ATOM ***** C32 PS 800 75.332 81.456 -19.951 1.00 0.00
>> MEMB
>>>> ATOM ***** H2A PS 800 76.379 81.622 -20.157 1.00 0.00
>> MEMB
>>>> ATOM ***** C33 PS 800 74.946 80.192 -20.789 1.00 0.00
>> MEMB
>>>> ATOM ***** O35 PS 800 73.870 80.247 -21.484 1.00 0.00
>> MEMB
>>>> ATOM ***** O36 PS 800 75.649 79.158 -20.734 1.00 0.00
>> MEMB
>>>> ATOM ***** C31 PS 800 75.115 81.146 -18.434 1.00 0.00
>> MEMB
>>>> ATOM ***** H1A PS 800 74.014 81.127 -18.285 1.00 0.00
>> MEMB
>>>> ATOM ***** H1B PS 800 75.411 82.068 -17.891 1.00 0.00
>> MEMB
>>>> ATOM ***** P31 PS 800 77.239 79.834 -17.504 1.00 0.00
>> MEMB
>>>> ATOM ***** O33 PS 800 78.065 80.151 -18.660 1.00 0.00
>> MEMB
>>>> ATOM ***** O34 PS 800 77.571 78.619 -16.699 1.00 0.00
>> MEMB
>>>> ATOM ***** O32 PS 800 75.765 79.985 -17.970 1.00 0.00
>> MEMB
>>>> ATOM ***** O31 PS 800 77.284 81.066 -16.547 1.00 0.00
>> MEMB
>>>> ATOM ***** C3 PS 800 78.525 81.521 -16.091 1.00 0.00
>> MEMB
>>>> ATOM ***** HA PS 800 78.302 82.478 -15.572 1.00 0.00
>> MEMB
>>>> ATOM ***** HB PS 800 79.256 81.763 -16.892 1.00 0.00
>> MEMB
>>>> ATOM ***** C2 PS 800 79.174 80.576 -15.042 1.00 0.00
>> MEMB
>>>> ATOM ***** HX PS 800 79.570 79.713 -15.618 1.00 0.00
>> MEMB
>>>> ATOM ***** O21 PS 800 78.261 80.110 -14.066 1.00 0.00
>> MEMB
>>>> ATOM ***** C21 PS 800 78.490 78.864 -13.657 1.00 0.00
>> MEMB
>>>> ATOM ***** O22 PS 800 79.325 78.127 -14.168 1.00 0.00
>> MEMB
>>>> ATOM ***** C1 PS 800 80.406 81.171 -14.310 1.00 0.00
>> MEMB
>>>> ATOM ***** HR PS 800 81.175 81.327 -15.097 1.00 0.00
>> MEMB
>>>> ATOM ***** HS PS 800 80.885 80.394 -13.678 1.00 0.00
>> MEMB
>>>> ATOM ***** O11 PS 800 80.052 82.375 -13.665 1.00 0.00
>> MEMB
>>>> ATOM ***** C11 PS 800 80.151 82.502 -12.307 1.00 0.00
>> MEMB
>>>> ATOM ***** O12 PS 800 80.330 81.659 -11.484 1.00 0.00
>> MEMB
>>>> ATOM ***** C12 OL 800 77.408 78.544 -12.625 1.00 0.00
>> MEMB
>>>> ATOM ***** H2R OL 800 76.845 77.747 -13.156 1.00 0.00
>> MEMB
>>>> ATOM ***** H2S OL 800 76.739 79.423 -12.508 1.00 0.00
>> MEMB
>>>> ATOM ***** C13 OL 800 78.143 78.124 -11.411 1.00 0.00
>> MEMB
>>>> ATOM ***** H3R OL 800 78.637 79.072 -11.108 1.00 0.00
>> MEMB
>>>> ATOM ***** H3S OL 800 78.877 77.302 -11.555 1.00 0.00
>> MEMB
>>>> ATOM ***** C14 OL 800 77.246 77.918 -10.171 1.00 0.00
>> MEMB
>>>> ATOM ***** H4R OL 800 76.503 78.742 -10.224 1.00 0.00
>> MEMB
>>>> ATOM ***** H4S OL 800 77.842 78.041 -9.241 1.00 0.00
>> MEMB
>>>> ATOM ***** C15 OL 800 76.632 76.505 -10.018 1.00 0.00
>> MEMB
>>>> ATOM ***** H5R OL 800 77.448 75.853 -10.398 1.00 0.00
>> MEMB
>>>> ATOM ***** H5S OL 800 75.808 76.429 -10.759 1.00 0.00
>> MEMB
>>>> ATOM ***** C16 OL 800 76.312 76.126 -8.596 1.00 0.00
>> MEMB
>>>> ATOM ***** H6R OL 800 77.163 76.343 -7.914 1.00 0.00
>> MEMB
>>>> ATOM ***** H6S OL 800 76.099 75.042 -8.487 1.00 0.00
>> MEMB
>>>> ATOM ***** C17 OL 800 74.938 76.755 -8.031 1.00 0.00
>> MEMB
>>>> ATOM ***** H7R OL 800 74.066 76.383 -8.610 1.00 0.00
>> MEMB
>>>> ATOM ***** H7S OL 800 74.933 77.865 -8.083 1.00 0.00
>> MEMB
>>>> ATOM ***** C18 OL 800 74.607 76.518 -6.615 1.00 0.00
>> MEMB
>>>> ATOM ***** H8R OL 800 74.594 75.427 -6.404 1.00 0.00
>> MEMB
>>>> ATOM ***** H8S OL 800 73.591 76.942 -6.465 1.00 0.00
>> MEMB
>>>> ATOM ***** C19 OL 800 75.576 77.205 -5.707 1.00 0.00
>> MEMB
>>>> ATOM ***** H9R OL 800 76.584 76.799 -5.879 1.00 0.00
>> MEMB
>>>> ATOM ***** C110 OL 800 75.248 78.097 -4.781 1.00 0.00
>> MEMB
>>>> ATOM ***** H10R OL 800 76.158 78.481 -4.296 1.00 0.00
>> MEMB
>>>> ATOM ***** C111 OL 800 73.858 78.617 -4.426 1.00 0.00
>> MEMB
>>>> ATOM ***** H11R OL 800 73.905 78.892 -3.351 1.00 0.00
>> MEMB
>>>> ATOM ***** H11S OL 800 73.169 77.751 -4.521 1.00 0.00
>> MEMB
>>>> ATOM ***** C112 OL 800 73.363 79.783 -5.257 1.00 0.00
>> MEMB
>>>> ATOM ***** H12R OL 800 72.331 79.990 -4.901 1.00 0.00
>> MEMB
>>>> ATOM ***** H12S OL 800 73.176 79.468 -6.306 1.00 0.00
>> MEMB
>>>> ATOM ***** C113 OL 800 74.160 81.056 -5.282 1.00 0.00
>> MEMB
>>>> ATOM ***** H13R OL 800 74.080 81.753 -6.144 1.00 0.00
>> MEMB
>>>> ATOM ***** H13S OL 800 75.241 80.801 -5.236 1.00 0.00
>> MEMB
>>>> ATOM ***** C114 OL 800 73.763 81.930 -4.128 1.00 0.00
>> MEMB
>>>> ATOM ***** H14R OL 800 74.010 81.422 -3.172 1.00 0.00
>> MEMB
>>>> ATOM ***** H14S OL 800 72.675 82.135 -4.230 1.00 0.00
>> MEMB
>>>> ATOM ***** C115 OL 800 74.694 83.179 -3.944 1.00 0.00
>> MEMB
>>>> ATOM ***** H15R OL 800 75.163 83.505 -4.897 1.00 0.00
>> MEMB
>>>> ATOM ***** H15S OL 800 75.619 82.839 -3.430 1.00 0.00
>> MEMB
>>>> ATOM ***** C116 OL 800 74.085 84.334 -3.164 1.00 0.00
>> MEMB
>>>> ATOM ***** H16R OL 800 73.533 83.861 -2.323 1.00 0.00
>> MEMB
>>>> ATOM ***** H16S OL 800 73.267 84.515 -3.893 1.00 0.00
>> MEMB
>>>> ATOM ***** C117 OL 800 74.968 85.522 -2.752 1.00 0.00
>> MEMB
>>>> ATOM ***** H17R OL 800 74.555 86.077 -1.883 1.00 0.00
>> MEMB
>>>> ATOM ***** H17S OL 800 75.099 86.195 -3.626 1.00 0.00
>> MEMB
>>>> ATOM ***** C118 OL 800 76.392 85.141 -2.336 1.00 0.00
>> MEMB
>>>> ATOM ***** H18R OL 800 77.011 84.768 -3.180 1.00 0.00
>> MEMB
>>>> ATOM ***** H18S OL 800 76.385 84.549 -1.396 1.00 0.00
>> MEMB
>>>> ATOM ***** H18T OL 800 76.866 86.102 -2.045 1.00 0.00
>> MEMB
>>>> TER
>>>> ATOM ***** O WAT 1 -68.879 -70.779 23.612 1.00 0.00
>> TIP3
>>>> ATOM ***** H1 WAT 1 -68.790 -69.835 23.480 1.00 0.00
>> TIP3
>>>> ATOM ***** H2 WAT 1 -69.517 -71.054 22.954 1.00 0.00
>> TIP3
>>>> ATOM ***** O WAT 2 -69.946 -71.524 27.031 1.00 0.00
>> TIP3
>>>> ATOM ***** H1 WAT 2 -69.984 -72.170 27.736 1.00 0.00
>> TIP3
>>>> ATOM ***** H2 WAT 2 -70.268 -71.990 26.260 1.00 0.00
>> TIP3
>>>> ATOM ***** O WAT 3 -77.577 -71.909 28.624 1.00 0.00
>> TIP3
>>>> ......
>>>> ATOM ***** H2 WAT 39999 58.478 70.625 -20.380 1.00 0.00
>> TIP3
>>>> ATOM ***** O WAT 40000 64.171 70.870 -19.653 1.00 0.00
>> TIP3
>>>> ATOM ***** H1 WAT 40000 64.247 70.965 -20.602 1.00 0.00
>> TIP3
>>>> ATOM ***** H2 WAT 40000 63.896 69.962 -19.524 1.00 0.00
>> TIP3
>>>> ATOM ***** K+ K+ 1 43.482 -66.336 61.767 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 2 -61.232 58.875 20.194 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 3 -32.974 -77.954 47.257 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 4 35.237 -64.006 54.392 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 5 33.710 -50.538 29.075 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 6 75.583 -28.140 23.951 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 7 32.500 0.424 23.564 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 8 -48.770 79.590 60.267 1.00 0.00
>> POT
>>>> ......
>>>> ATOM ***** K+ K+ 377 49.526 19.012 60.661 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 378 -64.872 0.648 30.202 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 379 51.206 -27.782 35.725 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 380 -80.185 -70.365 21.864 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 381 -6.077 -22.940 61.724 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 382 45.404 23.466 35.288 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 383 -37.648 -1.184 31.869 1.00 0.00
>> POT
>>>> ATOM ***** K+ K+ 384 13.934 53.910 27.076 1.00 0.00
>> POT
>>>> TER
>>>> END
>>>>
>>>>
>>>>
>>>> On Mon, Jan 11, 2016 at 12:34 AM, Jean-Marc <jmbillod.cib.csic.es>
>> wrote:
>>>>
>>>>> Hello,
>>>>> It is difficult to tell what is wrong without the pdb, could you please
>>>>> provide the one you're using? Did you try to load the pdb used in the
>>>>> tutorial into leap, does it work flawlessly?
>>>>> Best regards,
>>>>> Jean-Marc
>>>>>
>>>>>
>>>>>
>>>>> Sent from my iPhone
>>>>>> On 09 Jan 2016, at 23:40, Bin Wang <ben.wangbj.gmail.com> wrote:
>>>>>>
>>>>>> Dear Amber users,
>>>>>>
>>>>>> I followed the method in this website to install the AmberTools 15,
>> and
>>>>> try
>>>>>> to use the lipdi14 force field with Amber 11
>>>>>> http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
>>>>>>
>>>>>> Then I followed the Amber online tutorial 16 to get the
>> membrane-protein
>>>>>> structure.
>>>>>> http://ambermd.org/tutorials/advanced/tutorial16/
>>>>>>
>>>>>> However, when I used xleap to load the pdb file of this
>> membrane-protein
>>>>>> structure, the xleap showed a lot of errors such as these:
>>>>>>
>>>>>> Created a new atom named: C11 within residue: .R<PS 1969>
>>>>>> Created a new atom named: O12 within residue: .R<PS 1969>
>>>>>> One sided connection. Residue: default_name missing connect1 atom.
>>>>>> Creating new UNIT for residue: PS sequence: 1972
>>>>>> One sided connection. Residue: missing connect0 atom.
>>>>>> Created a new atom named: N31 within residue: .R<PS 1972>
>>>>>> Created a new atom named: HN1A within residue: .R<PS 1972>
>>>>>> Created a new atom named: HN1B within residue: .R<PS 1972>
>>>>>> Created a new atom named: HN1C within residue: .R<PS 1972>
>>>>>> Created a new atom named: C32 within residue: .R<PS 1972>
>>>>>> Created a new atom named: H2A within residue: .R<PS 1972>
>>>>>> Created a new atom named: C33 within residue: .R<PS 1972>
>>>>>> Created a new atom named: O35 within residue: .R<PS 1972>
>>>>>> Created a new atom named: O36 within residue: .R<PS 1972>
>>>>>>
>>>>>>
>>>>>> It seems that the xleap doesn't recognize the PS and PA lipid units in
>>>>> the
>>>>>> pdb file. I think I followed every step according to these tutorials,
>> but
>>>>>> couldn't find out why it didn't work.
>>>>>>
>>>>>> Could anybody give me some suggestions? Thank you very much!
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>
>>
>>
>>
>> _______________________________________________
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Received on Mon Jan 11 2016 - 21:30:04 PST
