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

[Bhawana Gupta]

hello,
thankyou for ur advice on the mail named *missing of methyl at N-terminal.
*  i m using forcefield ffgmx. u had advice me to put the correct name for
terminal N-CH3 group
i.e. i had replaced NHM with NAC as given there. That error has been solved
but again i m getting the  error as:
---------------------------------------------------------
Program pdb2gmx, VERSION 4.0
Source code file: pdb2top.c, line: 574

Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
-----------------------------------------------------

This is my pdb file in text editor

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   NAC     6      10.022   9.633  -1.069  1.00  0.00
N
ATOM     25  CA  NAC     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

so pls help me out.
i had taken my pdb file from INSIGHTII program.

With Regards
Bhawana
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