[gmx-users] missing of methyl at N-terminal

[Bhawana Gupta]

thankyou for ur reply.
exact error which i m getting, when running pdb2gmx command with the pdb
which i had taken from insightII is
Program pdb2gmx, VERSION 4.0
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C in residue NH2 6 not found in rtp entry with 3 atoms
             while sorting atoms


this is my pdb in text editor
there is a presence of 25 atom in my pdb (C in residue NH2 6), but i m
getting the error mentioned above
AUTHOR    GENERATED BY OPEN BABEL 2.2.0
ATOM      1  CA  ACE     1      -3.811  -0.502   0.471  1.00  0.00
C
ATOM      2  C   ACE     1      -2.354  -0.410   0.072  1.00  0.00
C
ATOM      3  O   ACE     1      -1.743  -1.403  -0.345  1.00  0.00
O
ATOM      4  N   ALA     2      -1.649   0.885   0.183  1.00  0.00
N
ATOM      5  CA  ALA     2      -0.244   1.035  -0.187  1.00  0.00
C
ATOM      6  C   ALA     2       0.221   2.456   0.023  1.00  0.00
C
ATOM      7  O   ALA     2      -0.530   3.334   0.466  1.00  0.00
O
ATOM      8  CB  ALA     2      -0.094   0.568  -1.645  1.00  0.00
C
ATOM      9  N   ALA     3       1.482   2.703  -0.281  1.00  0.00
N
ATOM     10  CA  ALA     3       2.069   4.031  -0.129  1.00  0.00
C
ATOM     11  C   ALA     3       3.519   4.033  -0.548  1.00  0.00
C
ATOM     12  O   ALA     3       4.081   3.015  -0.969  1.00  0.00
O
ATOM     13  CB  ALA     3       1.870   4.463   1.334  1.00  0.00
C
ATOM     14  N   ALA     4       4.149   5.189  -0.449  1.00  0.00
N
ATOM     15  CA  ALA     4       5.553   5.340  -0.819  1.00  0.00
C
ATOM     16  C   ALA     4       6.019   6.761  -0.609  1.00  0.00
C
ATOM     17  O   ALA     4       5.267   7.638  -0.166  1.00  0.00
O
ATOM     18  CB  ALA     4       5.704   4.872  -2.277  1.00  0.00
C
ATOM     19  N   ALA     5       7.279   7.008  -0.913  1.00  0.00
N
ATOM     20  CA  ALA     5       7.866   8.336  -0.760  1.00  0.00
C
ATOM     21  C   ALA     5       9.317   8.337  -1.179  1.00  0.00
C
ATOM     22  O   ALA     5       9.879   7.319  -1.601  1.00  0.00
O
ATOM     23  CB  ALA     5       7.668   8.768   0.703  1.00  0.00
C
ATOM     24  N   NHM     6      10.022   9.633  -1.069  1.00  0.00
N
ATOM     25  C   NHM     6      11.417   9.736  -1.462  1.00  0.00
C
CONECT    1    2
CONECT    2    3    4    1
CONECT    3    2
CONECT    4    5    2
CONECT    5    8    6    4
CONECT    6    9    5    7
CONECT    7    6
CONECT    8    5
CONECT    9   10    6
CONECT   10   11    9   13
CONECT   11   12   14   10
CONECT   12   11
CONECT   13   10
CONECT   14   15   11
CONECT   15   18   16   14
CONECT   16   19   15   17
CONECT   17   16
CONECT   18   15
CONECT   19   20   16
CONECT   20   21   19   23
CONECT   21   22   24   20
CONECT   22   21
CONECT   23   20
CONECT   24   25   21
CONECT   25   24
MASTER        0    0    0    0    0    0    0    0   25    0   25    0
END

Please help me out.

With regards
Bhawana
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