Fwd: [gmx-users] The .pdb file compatible with structure of .itp file,

[Ali Alizadeh]

Dear Justin

Thank you for your reply.
But i knew that,
i have a .itp file for example: heptane.itp:

[ moleculetype ]
; Name  nrexcl
HEP     3

[ atoms ]
; nr    type    resnr   residu  atom    cgnr    charge
1       CH3     1       LIG     CH31    1       0.0
2       CH2     1       LIG     CH22    2       0.0
3       CH2     1       LIG     CH23    3       0.0
4       CH2     1       LIG     CH24    4       0.0
5       CH2     1       LIG     CH25    5       0.0
6       CH2     1       LIG     CH26    6       0.0
7       CH3     1       LIG     CH37    7       0.0
[ bonds ]
; i     j
1       2
2       3
3       4
4       5
5       6
6       7

[ angles ]
; i     j       k
1       2       3
2       3       4
3       4       5
4       5       6
5       6       7

[ dihedrals ]
; i     j       k       l       type
1       2       3       4       3
2       3       4       5       3
3       4       5       6       3
4       5       6       7       3

and my pdb file for heptane:

COMPND    UNNAMED
AUTHOR    GENERATED BY OPEN BABEL 2.3.0
ATOM      1  C   LIG     1      -5.231   0.634  -0.427  1.00  0.00
  C
ATOM      2  H   LIG     1      -5.407  -0.100  -1.242  1.00  0.00
  H
ATOM      3  H   LIG     1      -5.768   1.574  -0.673  1.00  0.00
  H
ATOM      4  H   LIG     1      -5.641   0.230   0.523  1.00  0.00
  H
ATOM      5  C   LIG     1      -3.739   0.920  -0.284  1.00  0.00
  C
ATOM      6  H   LIG     1      -3.595   1.672   0.522  1.00  0.00
  H
ATOM      7  H   LIG     1      -3.377   1.346  -1.242  1.00  0.00
  H
ATOM      8  C   LIG     1      -2.963  -0.360   0.064  1.00  0.00
  C
ATOM      9  H   LIG     1      -3.379  -0.775   1.009  1.00  0.00
  H
ATOM     10  H   LIG     1      -3.101  -1.119  -0.737  1.00  0.00
  H
ATOM     11  C   LIG     1      -0.728   0.352  -0.983  1.00  0.00
  C
ATOM     12  H   LIG     1      -0.896  -0.406  -1.780  1.00  0.00
  H
ATOM     13  H   LIG     1      -1.130   1.324  -1.336  1.00  0.00
  H
ATOM     14  C   LIG     1       0.790   0.492  -0.786  1.00  0.00
  C
ATOM     15  H   LIG     1       1.220  -0.478  -0.454  1.00  0.00
  H
ATOM     16  H   LIG     1       1.242   0.752  -1.768  1.00  0.00
  H
ATOM     17  C   LIG     1      -1.461  -0.115   0.288  1.00  0.00
  C
ATOM     18  H   LIG     1      -1.340   0.624   1.106  1.00  0.00
  H
ATOM     19  H   LIG     1      -1.009  -1.077   0.616  1.00  0.00
  H
ATOM     20  C   LIG     1       1.172   1.589   0.209  1.00  0.00
  C
ATOM     21  H   LIG     1       0.797   1.360   1.226  1.00  0.00
  H
ATOM     22  H   LIG     1       0.764   2.568  -0.123  1.00  0.00
  H
ATOM     23  H   LIG     1       2.278   1.667   0.264  1.00  0.00
  H

Above file is only for one molecule.

How to i use this pdb file for the .itp file ?(If i have 1000 heptane
molecules)
Can I use VMD software?

Sincerely