I got so many atoms in one residue

This topic has 3 replies, 3 voices, and was last updated 4 years, 9 months ago by Anonymous.

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- March 24, 2020 at 11:40 am #3380
  Anonymous
  Hello,
  
  When i use AbinitioRelax locally,i got the result .pdb file with so many atoms in one residue as below:
  
  ATOM 1 N SER A 1 0.000 0.000 0.000 1.00 0.00 N
  
  ATOM 2 CA SER A 1 1.458 0.000 0.000 1.00 0.00 C
  
  ATOM 3 C SER A 1 2.009 1.420 0.000 1.00 0.00 C
  
  ATOM 4 O SER A 1 1.383 2.339 -0.529 1.00 0.00 O
  
  ATOM 5 CB SER A 1 1.980 -0.754 -1.207 1.00 0.00 C
  
  ATOM 6 OG SER A 1 1.610 -0.115 -2.398 1.00 0.00 O
  
  ATOM 7 1H SER A 1 -0.334 -0.943 -0.000 1.00 0.00 H
  
  ATOM 8 2H SER A 1 -0.334 0.471 0.816 1.00 0.00 H
  
  ATOM 9 3H SER A 1 -0.334 0.471 -0.816 1.00 0.00 H
  
  ATOM 10 HA SER A 1 1.804 -0.502 0.905 1.00 0.00 H
  
  ATOM 11 1HB SER A 1 3.066 -0.824 -1.151 1.00 0.00 H
  
  ATOM 12 2HB SER A 1 1.586 -1.770 -1.200 1.00 0.00 H
  
  ATOM 13 HG SER A 1 1.406 0.793 -2.158 1.00 0.00 H
  
  ATOM 14 N ASN A 2 3.184 1.594 0.596 1.00 0.00 N
  
  ATOM 15 CA ASN A 2 3.821 2.903 0.666 1.00 0.00 C
  
  ATOM 16 C ASN A 2 5.339 2.776 0.690 1.00 0.00 C
  
  ATOM 17 O ASN A 2 5.881 1.789 1.186 1.00 0.00 O
  
  ATOM 18 CB ASN A 2 3.331 3.672 1.879 1.00 0.00 C
  
  ATOM 19 CG ASN A 2 3.698 5.129 1.827 1.00 0.00 C
  
  ATOM 20 OD1 ASN A 2 4.222 5.614 0.818 1.00 0.00 O
  
  ATOM 21 ND2 ASN A 2 3.433 5.836 2.896 1.00 0.00 N
  
  ATOM 22 H ASN A 2 3.647 0.798 1.012 1.00 0.00 H
  
  ATOM 23 HA ASN A 2 3.558 3.465 -0.232 1.00 0.00 H
  
  ATOM 24 1HB ASN A 2 2.246 3.585 1.951 1.00 0.00 H
  
  ATOM 25 2HB ASN A 2 3.755 3.234 2.783 1.00 0.00 H
  
  ATOM 26 1HD2 ASN A 2 3.656 6.811 2.918 1.00 0.00 H
  
  ATOM 27 2HD2 ASN A 2 3.009 5.402 3.690 1.00 0.00 H
  
  ATOM 28 N ALA A 3 6.020 3.781 0.150 1.00 0.00 N
  
  ATOM 29 CA ALA A 3 7.478 3.784 0.108 1.00 0.00 C
  
  ATOM 30 C ALA A 3 8.028 5.203 0.158 1.00 0.00 C
  
  ATOM 31 O ALA A 3 7.387 6.144 -0.310 1.00 0.00 O
  
  ATOM 32 CB ALA A 3 7.973 3.068 -1.140 1.00 0.00 C
  
  ATOM 33 H ALA A 3 5.515 4.564 -0.241 1.00 0.00 H
  
  ATOM 34 HA ALA A 3 7.843 3.253 0.988 1.00 0.00 H
  
  ATOM 35 1HB ALA A 3 9.063 3.078 -1.157 1.00 0.00 H
  
  ATOM 36 2HB ALA A 3 7.620 2.036 -1.132 1.00 0.00 H
  
  ATOM 37 3HB ALA A 3 7.592 3.575 -2.025 1.00 0.00 H
  
  13 atoms in the first residue !!
  
  However,when i look up the result in casp13 from “BAKER”(086),one of the top5 model as follows:
  
  ATOM 1 N SER 1 6.928 6.372 23.607 1.00 3.89 N
  
  ATOM 2 CA SER 1 7.251 7.206 22.458 1.00 3.89 C
  
  ATOM 3 C SER 1 8.158 8.357 22.874 1.00 3.89 C
  
  ATOM 4 O SER 1 8.908 8.251 23.844 1.00 3.89 O
  
  ATOM 5 CB SER 1 5.972 7.752 21.843 1.00 5.83 C
  
  ATOM 6 OG SER 1 6.239 8.441 20.656 1.00 5.83 O
  
  ATOM 14 N ASN 2 8.070 9.460 22.146 1.00 3.89 N
  
  ATOM 15 CA ASN 2 8.848 10.653 22.452 1.00 3.89 C
  
  ATOM 16 C ASN 2 8.124 11.460 23.533 1.00 3.89 C
  
  ATOM 17 O ASN 2 7.036 11.088 23.976 1.00 3.89 O
  
  ATOM 18 CB ASN 2 9.047 11.455 21.159 1.00 5.83 C
  
  ATOM 19 CG ASN 2 10.235 12.414 21.128 1.00 5.83 C
  
  ATOM 20 OD1 ASN 2 10.649 12.983 22.153 1.00 5.83 O
  
  ATOM 21 ND2 ASN 2 10.784 12.600 19.953 1.00 5.83 N
  
  ATOM 28 N ALA 3 8.717 12.576 23.931 1.00 3.63 N
  
  ATOM 29 CA ALA 3 8.143 13.477 24.916 1.00 3.28 C
  
  ATOM 30 C ALA 3 6.850 14.048 24.388 1.00 2.59 C
  
  ATOM 31 O ALA 3 6.753 14.357 23.204 1.00 2.48 O
  
  ATOM 32 CB ALA 3 9.109 14.609 25.221 1.00 4.92 C
  
  which only 6 in the first res
  
  I use the default seeting as below(AbinitioRelax application):
  
  -in:file:fasta ./T0957s2.fasta
  
  -in:file:frag3 ./aaT0957s2A03_05.200_v1_3
  
  -in:file:frag9 ./aaT0957s2A09_05.200_v1_3
  
  -abinitio:relax
  
  -nstruct 20
  
  -out:pdb
  
  -use_filters true
  
  -psipred_ss2 ./T0957s2.psipred_ss2
  
  -abinitio::increase_cycles 10
  
  -abinitio::rg_reweight 0.5
  
  -abinitio::rsd_wt_helix 0.5
  
  -abinitio::rsd_wt_loop 0.5
  
  -relax::fast
  
  Is there someting wrong with seeting? And how to get the result as “BAKER” target with the same lenth?
- March 24, 2020 at 7:36 pm #15224
  Anonymous
  Hydrogens are needed in Rosetta and in Force field calculations in general.
  
  The first residue is correct. The second is not. You need to set -no_optH false as this is true by default. As the argument says you should NOT NOT do the optional step of adding hydrogens.
  - March 24, 2020 at 10:08 pm #15225
    Anonymous
    optH should be optimizing (packing, mostly) hydrogens, not adding them.
    
    You do not have a choice about adding them. Rosetta’s concept of alanine is with hydrogens in place. If you want to remove a hydrogen it’s no longer alanine, it’s a patched version of alanine. The PDB reader is just aware that atoms are missing in the input and tries to match stuff to the most likely intended residue (between the 3LCs, extant atoms, and whether it is a chain boundary, etc).
    
    As Matteo says, the 13 atom version is correct, you need the hydrogens at modeling time and they may as well be in the output. PDBs without most of the hydrogens – especially CASP stuff – may be in “centroid” mode (do you see CEN atoms?) – this is a “reduced representation” (chemistry reverse pun unintended) where the sidechain is represented by a big soft CEN atom, and most hydrogens are ignored. The CEN scorefunction is balanced for speed over accuracy.
  - March 25, 2020 at 2:35 am #15226
    Anonymous
    Thank you for help！ And I want to know ，dose this afferct the GDT-TS? As you see, the model rosetta give in casp do not have many optH
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