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
> >> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jan 11 2016 - 15:00:03 PST
