Dear Amber users,
I have encounter problems about defect residues of my receptor (a RNA
molecule, riboswitch), and I am looking for any suggestion to repair these
bad RNA residues.
Three Uracil and one Cytosine lose their bases in the original receptor
structure file. I used Chimera to add H, then imported the structure with
hydrogen information to xleap. Even if xleap added missing atoms to make U
and C bases to the bad residues, the strange hydrogen, whose symbol is H1'
' generated by Chimera, cannot be recognized by xleap and cause failure to
produce prmtop and inpcrd files. I am wondering if anyone would like to
share his experience or guidance to handle/repair these defect U and C
residues. I paste:
1. the information of the original versions of defect U and R residues
2. the version after add hydrogen by Chimera
3. the normal U and C residues
4. the error message of xleap related to this defect U and C
for your reference.
Thank you so much first for any suggestion.
Sincerely,
Crystal
=============Here is the original version of defect U and
C===========================
defect U:
ATOM 734 P U A 46 5.536 38.757 55.671 1.00103.94 P
ATOM 735 OP1 U A 46 5.102 39.580 54.507 1.00102.98 O
ATOM 736 OP2 U A 46 4.516 38.157 56.585 1.00102.35 O
ATOM 737 O5' U A 46 6.481 37.597 55.113 1.00103.26 O
ATOM 738 C5' U A 46 7.265 37.796 53.939 1.00103.65 C
ATOM 739 C4' U A 46 6.970 36.721 52.916 1.00104.43 C
ATOM 740 O4' U A 46 5.555 36.740 52.567 1.00106.62 O
ATOM 741 C3' U A 46 7.683 36.914 51.587 1.00103.99 C
ATOM 742 O3' U A 46 8.998 36.375 51.647 1.00100.24 O
ATOM 743 C2' U A 46 6.781 36.161 50.612 1.00105.37 C
ATOM 744 O2' U A 46 6.988 34.758 50.621 1.00106.45 O
ATOM 745 C1' U A 46 5.395 36.481 51.178 1.00106.00 C
defect C:
ATOM 905 P C A 55 35.885 38.096 55.085 1.00120.00 P
ATOM 906 OP1 C A 55 35.675 37.212 53.904 1.00120.00 O
ATOM 907 OP2 C A 55 36.224 39.531 54.871 1.00119.48 O
ATOM 908 O5' C A 55 34.553 38.048 55.970 1.00117.70 O
ATOM 909 C5' C A 55 34.468 38.712 57.238 1.00112.73 C
ATOM 910 C4' C A 55 33.293 39.681 57.262 1.00109.50 C
ATOM 911 O4' C A 55 33.584 40.831 56.420 1.00108.79 O
ATOM 912 C3' C A 55 31.957 39.159 56.742 1.00106.73 C
ATOM 913 O3' C A 55 31.200 38.443 57.721 1.00100.06 O
ATOM 914 C2' C A 55 31.227 40.435 56.334 1.00107.38 C
ATOM 915 O2' C A 55 30.532 41.047 57.409 1.00106.32 O
ATOM 916 C1' C A 55 32.383 41.311 55.834 1.00107.87 C
====================================================================
==========the version after add hydrogen by Chimera, which generate weird
H1' '===============
defect U:
ATOM 1104 P U A 46 5.536 38.757 55.671 1.00103.94 P
ATOM 1105 OP1 U A 46 5.102 39.580 54.507 1.00102.98 O
ATOM 1106 OP2 U A 46 4.516 38.157 56.585 1.00102.35 O
ATOM 1107 O5' U A 46 6.481 37.597 55.113 1.00103.26 O
ATOM 1108 C5' U A 46 7.265 37.796 53.939 1.00103.65 C
ATOM 1109 C4' U A 46 6.970 36.721 52.916 1.00104.43 C
ATOM 1110 O4' U A 46 5.555 36.740 52.567 1.00106.62 O
ATOM 1111 C3' U A 46 7.683 36.914 51.587 1.00103.99 C
ATOM 1112 O3' U A 46 8.998 36.375 51.647 1.00100.24 O
ATOM 1113 C2' U A 46 6.781 36.161 50.612 1.00105.37 C
ATOM 1114 O2' U A 46 6.988 34.758 50.621 1.00106.45 O
ATOM 1115 C1' U A 46 5.395 36.481 51.178 1.00106.00 C
ATOM 1116 H5' U A 46 8.322 37.759 54.203 1.00 0.00 H
ATOM 1117 H5'' U A 46 7.034 38.772 53.513 1.00 0.00 H
ATOM 1118 H4' U A 46 7.229 35.746 53.329 1.00 0.00 H
ATOM 1119 H3' U A 46 7.720 37.972 51.328 1.00 0.00 H
ATOM 1120 H2' U A 46 6.887 36.560 49.603 1.00 0.00 H
ATOM 1121 HO2' U A 46 7.858 34.560 50.266 1.00 0.00 H
ATOM 1122 H1' U A 46 4.727 35.632 51.031 1.00 0.00 H
ATOM 1123 H1'' U A 46 4.987 37.362 50.682 1.00 0.00 H
defect C:
ATOM 1367 P C A 55 35.885 38.096 55.085 1.00120.00 P
ATOM 1368 OP1 C A 55 35.675 37.212 53.904 1.00120.00 O
ATOM 1369 OP2 C A 55 36.224 39.531 54.871 1.00119.48 O
ATOM 1370 O5' C A 55 34.553 38.048 55.970 1.00117.70 O
ATOM 1371 C5' C A 55 34.468 38.712 57.238 1.00112.73 C
ATOM 1372 C4' C A 55 33.293 39.681 57.262 1.00109.50 C
ATOM 1373 O4' C A 55 33.584 40.831 56.420 1.00108.79 O
ATOM 1374 C3' C A 55 31.957 39.159 56.742 1.00106.73 C
ATOM 1375 O3' C A 55 31.200 38.443 57.721 1.00100.06 O
ATOM 1376 C2' C A 55 31.227 40.435 56.334 1.00107.38 C
ATOM 1377 O2' C A 55 30.532 41.047 57.409 1.00106.32 O
ATOM 1378 C1' C A 55 32.383 41.311 55.834 1.00107.87 C
ATOM 1379 H5' C A 55 34.334 37.968 58.023 1.00 0.00 H
ATOM 1380 H5'' C A 55 35.392 39.262 57.418 1.00 0.00 H
ATOM 1381 H4' C A 55 33.153 40.029 58.285 1.00 0.00 H
ATOM 1382 H3' C A 55 32.120 38.530 55.867 1.00 0.00 H
ATOM 1383 H2' C A 55 30.538 40.225 55.516 1.00 0.00 H
ATOM 1384 HO2' C A 55 29.818 40.474 57.696 1.00 0.00 H
ATOM 1385 H1' C A 55 32.216 42.347 56.129 1.00 0.00 H
ATOM 1386 H1'' C A 55 32.452 41.245 54.748 1.00 0.00 H
========================================
===The normal U and C, without problems in xleap===
normal U:
ATOM 359 P U A 20 18.791 34.106 68.474 1.00 69.72 P
ATOM 360 OP1 U A 20 19.428 34.240 69.815 1.00 67.94 O
ATOM 361 OP2 U A 20 18.187 32.810 68.067 1.00 70.75 O
ATOM 362 O5' U A 20 17.683 35.246 68.307 1.00 67.65 O
ATOM 363 C5' U A 20 18.093 36.593 68.325 1.00 64.78 C
ATOM 364 C4' U A 20 16.943 37.551 68.143 1.00 64.09 C
ATOM 365 O4' U A 20 16.536 37.558 66.739 1.00 64.68 O
ATOM 366 C3' U A 20 15.688 37.146 68.888 1.00 63.48 C
ATOM 367 O3' U A 20 15.246 37.686 70.094 1.00 67.10 O
ATOM 368 C2' U A 20 14.684 36.585 67.920 1.00 64.08 C
ATOM 369 O2' U A 20 13.488 37.305 68.143 1.00 63.57 O
ATOM 370 C1' U A 20 15.207 37.089 66.591 1.00 63.02 C
ATOM 371 N1 U A 20 15.102 36.075 65.536 1.00 61.23 N
ATOM 372 C2 U A 20 14.588 36.494 64.331 1.00 62.06 C
ATOM 373 O2 U A 20 14.302 37.658 64.111 1.00 64.97 O
ATOM 374 N3 U A 20 14.411 35.508 63.394 1.00 60.85 N
ATOM 375 C4 U A 20 14.693 34.182 63.536 1.00 58.57 C
ATOM 376 O4 U A 20 14.457 33.425 62.604 1.00 61.36 O
ATOM 377 C5 U A 20 15.247 33.818 64.806 1.00 58.86 C
ATOM 378 C6 U A 20 15.438 34.759 65.739 1.00 59.39 C
ATOM 379 H5' U A 20 18.571 36.800 69.282 1.00 0.00 H
ATOM 380 H5'' U A 20 18.817 36.753 67.526 1.00 0.00 H
ATOM 381 H4' U A 20 17.245 38.554 68.445 1.00 0.00 H
ATOM 382 H3' U A 20 16.054 36.198 69.281 1.00 0.00 H
ATOM 383 H2' U A 20 14.570 35.502 67.973 1.00 0.00 H
ATOM 384 HO2' U A 20 13.100 37.032 68.978 1.00 0.00 H
ATOM 385 H1' U A 20 14.590 37.937 66.295 1.00 0.00 H
ATOM 386 H3 U A 20 14.031 35.795 62.503 1.00 0.00 H
ATOM 387 H5 U A 20 15.509 32.790 65.010 1.00 0.00 H
ATOM 388 H6 U A 20 15.872 34.473 66.686 1.00 0.00 H
normal C:
ATOM 192 P C A 15 13.292 26.611 45.052 1.00 82.84 P
ATOM 193 OP1 C A 15 12.035 25.821 45.182 1.00 83.07 O
ATOM 194 OP2 C A 15 13.309 28.039 45.494 1.00 81.33 O
ATOM 195 O5' C A 15 14.459 25.821 45.811 1.00 80.70 O
ATOM 196 C5' C A 15 14.689 24.434 45.558 1.00 78.27 C
ATOM 197 C4' C A 15 16.044 24.011 46.083 1.00 77.99 C
ATOM 198 O4' C A 15 17.080 24.778 45.411 1.00 76.87 O
ATOM 199 C3' C A 15 16.325 24.253 47.559 1.00 78.96 C
ATOM 200 O3' C A 15 15.798 23.232 48.398 1.00 81.22 O
ATOM 201 C2' C A 15 17.847 24.243 47.588 1.00 76.78 C
ATOM 202 O2' C A 15 18.386 22.940 47.549 1.00 77.07 O
ATOM 203 C1' C A 15 18.169 24.998 46.299 1.00 74.72 C
ATOM 204 N1 C A 15 18.255 26.436 46.573 1.00 71.17 N
ATOM 205 C2 C A 15 19.430 26.945 47.117 1.00 69.58 C
ATOM 206 O2 C A 15 20.381 26.180 47.308 1.00 67.81 O
ATOM 207 N3 C A 15 19.502 28.255 47.424 1.00 69.23 N
ATOM 208 C4 C A 15 18.454 29.048 47.201 1.00 69.43 C
ATOM 209 N4 C A 15 18.562 30.338 47.532 1.00 72.18 N
ATOM 210 C5 C A 15 17.248 28.557 46.631 1.00 68.13 C
ATOM 211 C6 C A 15 17.195 27.259 46.328 1.00 68.61 C
ATOM 212 H5' C A 15 13.915 23.847 46.053 1.00 0.00 H
ATOM 213 H5'' C A 15 14.647 24.253 44.484 1.00 0.00 H
ATOM 214 H4' C A 15 16.192 22.953 45.865 1.00 0.00 H
ATOM 215 H3' C A 15 15.945 25.228 47.863 1.00 0.00 H
ATOM 216 H2' C A 15 18.219 24.787 48.456 1.00 0.00 H
ATOM 217 HO2' C A 15 19.339 22.991 47.449 1.00 0.00 H
ATOM 218 H1' C A 15 19.099 24.634 45.863 1.00 0.00 H
ATOM 219 H41 C A 15 19.419 30.685 47.937 1.00 0.00 H
ATOM 220 H42 C A 15 17.786 30.966 47.377 1.00 0.00 H
ATOM 221 H5 C A 15 16.407 29.210 46.450 1.00 0.00 H
ATOM 222 H6 C A 15 16.299 26.853 45.882 1.00 0.00 H
==================================================
===error message of xleap when generate prmtop and inpcrd files===
Created a new atom named: H1'' within residue: .R<RU 43>
Added missing heavy atom: .R<RU 43>.A<N1 13>
Added missing heavy atom: .R<RU 43>.A<C6 14>
Added missing heavy atom: .R<RU 43>.A<C2 22>
Added missing heavy atom: .R<RU 43>.A<C5 16>
Added missing heavy atom: .R<RU 43>.A<N3 20>
Added missing heavy atom: .R<RU 43>.A<O2 23>
Added missing heavy atom: .R<RU 43>.A<C4 18>
Added missing heavy atom: .R<RU 43>.A<O4 19>
Created a new atom named: H1'' within residue: .R<RC 52>
Added missing heavy atom: .R<RC 52>.A<N1 13>
Added missing heavy atom: .R<RC 52>.A<C6 14>
Added missing heavy atom: .R<RC 52>.A<C2 23>
Added missing heavy atom: .R<RC 52>.A<C5 16>
Added missing heavy atom: .R<RC 52>.A<N3 22>
Added missing heavy atom: .R<RC 52>.A<O2 24>
Added missing heavy atom: .R<RC 52>.A<C4 18>
Added missing heavy atom: .R<RC 52>.A<N4 19>
> saveamberparm 2hom test.prmtop test.inpcrd
Checking Unit.
WARNING: There is a bond of 8.309758 angstroms between:
------- .R<RU 25>.A<O3' 30> and .R<RG 26>.A<P 1>
WARNING: The unperturbed charge of the unit: -77.000000 is not zero.
FATAL: Atom .R<RU 43>.A<H1'' 31> does not have a type.
FATAL: Atom .R<RU 51>.A<H1'' 31> does not have a type.
FATAL: Atom .R<RC 52>.A<H1'' 32> does not have a type.
FATAL: Atom .R<RU 76>.A<H1'' 31> does not have a type.
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Received on Mon Nov 21 2011 - 19:00:03 PST
