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I got so many atoms in one residue

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I got so many atoms in one residue
#1

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?

 

Post Situation: 
Tue, 2020-03-24 04:40
ylwang

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.

Tue, 2020-03-24 12:36
matteoferla

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.

Tue, 2020-03-24 15:08
smlewis

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

Tue, 2020-03-24 19:35
ylwang