[gmx-users] pdb2gmx problem

[Vivek Raut]

following is the .pdb file i give as input:

REMARK   4 

REMARK   4 LYSI COMPLIES WITH FORMAT V. 2.0, 
20-MAY-2003
ATOM      1  C   MTYL     1      7.844  -6.601  -8.462  0.00  0.00 
  C
ATOM      2  C   MTYL     1      3.503  -6.594  -5.983  0.00  0.00 
  C
ATOM      3  C   MTYL     1     -0.839  -6.587  -3.503  0.00  0.00 
  C
ATOM      4  C   MTYL     1     -0.815  -6.633  -8.503  0.00  0.00 
  C
ATOM      5  C   MTYL     1     -9.476  -6.575  -8.543  0.00  0.00 
  C
ATOM      6  C   MTYL     1     -5.181  -6.580  -1.023  0.00  0.00 
  C
ATOM      7  C   MTYL     1     -9.522  -6.573   1.456  0.00  0.00 
  C
ATOM      8  C   MTYL     1     -5.157  -6.626  -6.023  0.00  0.00 
  C
ATOM      9  C   MTYL     1     -9.499  -6.619  -3.543  0.00  0.00 
  C
ATOM     10  C   MTYL     1      7.798  -6.629   1.538  0.00  0.00 
  C
ATOM     11  C   MTYL     1      7.821  -6.676  -3.462  0.00  0.00 
  C
ATOM     12  C   MTYL     1      3.456  -6.622   4.017  0.00  0.00 
  C
ATOM     13  C   MTYL     1     -0.886  -6.615   6.497  0.00  0.00 
  C
ATOM     14  C   MTYL     1      3.479  -6.669  -0.982  0.00  0.00 
  C
ATOM     15  C   MTYL     1     -0.862  -6.661   1.497  0.00  0.00 
  C
ATOM     16  C   MTYL     1      7.774  -6.674   6.538  0.00  0.00 
  C
ATOM     17  C   MTYL     1      3.433  -6.666   9.017  0.00  0.00 
  C
ATOM     18  C   MTYL     1     -5.228  -6.608   8.977  0.00  0.00 
  C
ATOM     19  C   MTYL     1     -5.204  -6.654   3.977  0.00  0.00 
  C
ATOM     20  C   MTYL     1     -9.546  -6.647   6.457  0.00  0.00 
  C
TER
ATOM     21  N   LYS      1       1.225   0.626   1.344  1.00  0.00 
   N
ATOM     22  CA  LYS      1       2.680   0.748   1.344  1.00  0.00 
   C
ATOM     23  C   LYS      1       3.21    2.198   1.344  1.00  0.00 
   C
ATOM     24  O   LYS      1       2.282   3.34    1.344  1.00  0.00 
   O
ATOM     25  CB  LYS      1       3.295   0.003   0.122  1.00  0.00 
   C
ATOM     26  CG  LYS      1       4.851   0.029   0.085  1.00  0.00 
   C
ATOM     27  CD  LYS      1       5.489  -0.62   -1.156  1.00  0.00 
   C
ATOM     28  CE  LYS      1       7.019  -0.426  -1.23   1.00  0.00 
   C
ATOM     29  NZ  LYS      1       7.630  -1.052  -2.32   1.00  0.00 
   N
END

The residue type is added in ffgmx.rtp file as:

[ MTYL ]
  [ atoms ]
    C    C       0.01    1

but after using pdb2gmx, in output I see:

1MTYL     C    1   0.784  -0.660  -0.846
     2MTYL     C    2   0.350  -0.659  -0.598
     3MTYL     C    3   0.782  -0.668  -0.346
     4LYSH     N    4   0.122   0.500   0.600
     4LYSH    H1    5   0.042   0.490   0.541
     4LYSH    H2    6   0.101   0.561   0.676
     4LYSH    H3    7   0.198   0.538   0.547
     4LYSH    CA    8   0.268   0.000   0.800
     4LYSH    CB    9   0.329   0.500   0.300
     4LYSH    CG   10   0.485   0.100   0.900
     4LYSH    CD   11   0.548   0.900  -0.115
     4LYSH    CE   12   0.701   0.900   0.600
     4LYSH    NZ   13   0.763   0.000   0.200
     4LYSH   HZ1   14   0.789  -0.066   0.270
     4LYSH   HZ2   15   0.674  -0.026   0.161
     4LYSH   HZ3   16   0.832   0.000   0.128
     4LYSH     C   17   0.321   0.219   0.800
     4LYSH    O1   18   0.242   0.302   0.726
     4LYSH    O2   19   0.429   0.256   0.874

it reads only 2 MTYL atoms & ignores other 18. Also the coordinates are 
also changed. Why so?... & how do i rectify it?

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Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
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