[gmx-users] about rtp and pdb

[nanyu101]

Hi, David,

   I have already created rtp file manaul. Would you please check it for me,it's the first time I ever created rtp files.My polymer is CH3CO-Xn-OCH2CH3.I have created three rtp files.One is CH3CO-, the other is -X- residue,the last is -OCH2CH3.

[-X-]
 [atoms]
  C      C       0.180      1
  O      O     -0.180      1
  CA   CH2   0.000      2
  CB   CH     0.000      3
  CG   CH3   0.180     4
  OG   OS   -0.180     4

 [bonds]
  C      O
  C      CA
 -OG   C
  CA    CB
  CB    CG
  CB    OG
  [impropers]
   -O   C   O   CA
   -O -CA   C    O
   CA  CB  CG   OG
  
[-OCH2CH3]
 [atoms]
  OG   OS    -0.180     1
  CA   CH2    0.180     1
  CB   CH3    0.000     2

 [bonds]
  CA   CB
  CA   OG

[CH3CO-]
 [atoms] 
  C    C     0.180    1
  O       O    -0.180    1
  CA   CH3   0.000    2

 [bonds]
  C      O
  C      CA
 -OG   C

 [impropers]
 -O     C     O   CA
 -CB  OG   C    O



Are there something wrong?

After  I  finished creating rtp files,I have tried to use pdb2gmx to transfer pdb file to top and gro files.There are something wrong too. I hope it is not reason of wrong rtp files.

  The data of polymer is from ab initio calculation.Its pdb format is different from pdb file download from Protein Data Bank (Brookhaven National Labratory).I will show you two pieces of file respectively. First piece of file is from ab initio or Chem3D. The second piece of file is from Protein Data Bank.

HEADER
REMARK try
HETATM    1  C           1       0.000   0.000   0.000
HETATM    2  C           1       0.000   0.000   1.515
HETATM    3  O           1      -0.982  -0.013   2.214
HETATM    4  C           1       1.449  -0.016   3.429
HETATM    5  O           1       1.266   0.000   1.982
HETATM    6  C           1       1.418   1.405   3.968
HETATM    7  H           1      -1.013   0.076  -0.386
HETATM    8  H           1       0.628   0.821  -0.359
HETATM    9  H           1       0.484  -0.920  -0.341

..........................................





Second:

COMPND    ?
REMARK    File generated by Swiss-PdbViewer  3.70b0
REMARK    http://www.expasy.org/spdbv/
CRYST1   54.800   58.700   67.500  90.00  90.00  90.00 P 21 21 21    4   
ATOM      1  N   ILE    16      35.603  19.727  20.250  1.00 13.41
ATOM      2  CA  ILE    16      35.562  20.655  19.081  1.00 13.40
ATOM      3  C   ILE    16      36.798  20.420  18.264  1.00 13.62
ATOM      4  O   ILE    16      37.907  20.471  18.784  1.00 13.71
ATOM      5  CB  ILE    16      35.547  22.145  19.535  1.00 13.12
ATOM      6  CG1 ILE    16      34.314  22.418  20.479  1.00 14.86
ATOM      7  CG2 ILE    16      35.560  23.085  18.292  1.00 13.33
ATOM      8  CD1 ILE    16      32.952  22.518  19.778  1.00 13.96
ATOM      9  N   VAL    17      36.602  20.030  17.011  1.00 13.41
ATOM     10  CA  VAL    17      37.694  19.824  16.070  1.00 12.61
ATOM     11  C   VAL    17      37.835  21.083  15.227  1.00 12.59
ATOM     12  O   VAL    17      36.841  21.624  14.725  1.00 10.58
ATOM     13  CB  VAL    17      37.389  18.626  15.132  1.00 13.98
ATOM     14  CG1 VAL    17      38.528  18.432  14.158  1.00 12.06
ATOM     15  CG2 VAL    17      37.126  17.326  15.974  1.00 12.54
ATOM     16  N   GLY    18      39.060  21.590  15.138  1.00 12.26
ATOM     17  CA  GLY    18      39.328  22.714  14.263  1.00 14.63
ATOM     18  C   GLY    18      38.822  24.043  14.797  1.00 17.48
ATOM     19  O   GLY    18      38.541  24.963  14.023  1.00 17.10
ATOM     20  N   GLY    19      38.721  24.157  16.118  1.00 16.69
ATOM     21  CA  GLY    19      38.243  25.391  16.707  1.00 16.54


........................................



Could tell me what kind of factor made me failure, rtp files format or pdb file format? 



Thank you very much.



All your bests,

Xianhui Wu


 

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