Hi Jason,
Thank you for your suggestions. The reason I use Chimera to add H before
loading pdb to xleap is because the original file contains not only the
receptor, but also its ligand, which cannot be recognized and add H by
xleap. However, following your suggestion, I kept receptor and metal in the
original file but connection and ligand (I found connection caused xleap
crashed and failed to generate prmtop and inpcrd), xleap could successfully
load the receptor pdb file, add missing base U and C for the defect
residues, add H to all residues, and then generated prmtop and inpcrd files.
Probably the library all_nucleic94.lib includes the complete information of
hydrogen and other atoms of base and sugar, so xleap can add hydrogen and
base once it detects no hydrogen and no base information of defect
residues. I think for my case, I have to handle receptor + metal, and
ligand separately, then merge them together into one pdb for MD simulation.
Thank you again for your generous suggestion. I solved the problem by your
suggestion.
Sincerely,
Crystal
On Tue, Nov 22, 2011 at 3:53 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> Is there any reason you're not just using xleap to add hydrogens instead
> of chimera? Leap will add hydrogen atoms with the proper names for you.
>
> Alternatively, you can modify the names of the atoms to match the atom
> names in the library file that's being used (see files in
> $AMBERHOME/dat/leap/lib and the frcmod file you loaded in
> $AMBERHOME/dat/leap/cmd for which lib files were loaded).
>
> Also, the default names according to the pdb standard have changed for
> nucleic acids in the past couple years, so you should make sure you are
> using a modern NA force field for your system setup and simulations.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Nov 21, 2011, at 9:38 PM, "Crystal.CHIA-YU Ku" <
> crystal.chia.yu.gmail.com> wrote:
>
> > 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.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Nov 22 2011 - 15:00:03 PST
