[gmx-users] issue regarding gromacs software

suchita sakore suchitasakore00 at gmail.com
Sat Feb 16 11:42:36 CET 2019


as you mentioned in your reply according to that
my (peptide)PDB file contains some non-natural amino residue.
i am using command :
gmx_mpi pdb2gmx -f Mole.pdb -o pep.gro
the error is seen is:
[image: image.png]
i am attaching a file here:
REMARK   Accelrys Discovery Studio PDB file
REMARK   Created:  2019-02-16T13:33:38Z
MODEL        1
HETATM    1  C1  HNE     1       0.698   1.473   0.410  1.00  0.00
 C
HETATM    2  C2  HNE     1       1.657   0.454   0.353  1.00  0.00
 C
HETATM    3  C3  HNE     1       1.255  -0.887   0.354  1.00  0.00
 C
HETATM    4  C4  HNE     1      -0.106  -1.209   0.411  1.00  0.00
 C
HETATM    5  C5  HNE     1      -1.065  -0.191   0.467  1.00  0.00
 C
HETATM    6  C6  HNE     1      -0.663   1.150   0.467  1.00  0.00
 C
HETATM    7  N7  HNE     1       3.135   0.804   0.292  1.00  0.00
 N
HETATM    8  C8  HNE     1      -0.549  -2.684   0.411  1.00  0.00
 C
HETATM    9  H11 HNE     1       0.989   2.440   0.409  1.00  0.00
 H
HETATM   10  H12 HNE     1      -2.115  -0.439   0.511  1.00  0.00
 H
HETATM   11  H13 HNE     1      -1.402   1.936   0.510  1.00  0.00
 H
HETATM   12  C12 HNE     1       3.578   2.279   0.291  1.00  0.00
 C
HETATM   13  C13 HNE     1       5.114   2.355   0.223  1.00  0.00
 C
HETATM   14  N14 HNE     1       5.557   3.830   0.223  1.00  0.00
 N
HETATM   15  C15 HNE     1       7.094   3.906   0.155  1.00  0.00
 C
HETATM   16  C16 HNE     1       7.536   5.381   0.155  1.00  0.00
 C
HETATM   17  N17 HNE     1       9.073   5.456   0.087  1.00  0.00
 N
HETATM   18  C18 HNE     1       9.516   6.931   0.086  1.00  0.00
 C
HETATM   19  C19 HNE     1      11.052   7.007   0.018  1.00  0.00
 C
HETATM   20  N20 HNE     1      11.495   8.482   0.018  1.00  0.00
 N
HETATM   21  C21 HNE     1      13.031   8.557  -0.050  1.00  0.00
 C
HETATM   22  C22 HNE     1      13.474  10.032  -0.051  1.00  0.00
 C
HETATM   23  C23 HNE     1      15.011  10.108  -0.118  1.00  0.00
 C
HETATM   24  C24 HNE     1      15.453  11.583  -0.119  1.00  0.00
 C
HETATM   25  C25 HNE     1      16.990  11.658  -0.187  1.00  0.00
 C
HETATM   26  C26 HNE     1      17.432  13.133  -0.187  1.00  0.00
 C
HETATM   27  C27 HNE     1      18.969  13.209  -0.255  1.00  0.00
 C
HETATM   28  C28 HNE     1      19.412  14.684  -0.256  1.00  0.00
 C
HETATM   29  C29 HNE     1      20.948  14.759  -0.323  1.00  0.00
 C
HETATM   30  C30 HNE     1      21.391  16.234  -0.324  1.00  0.00
 C
HETATM   31  C31 HNE     1      22.928  16.310  -0.392  1.00  0.00
 C
HETATM   32  C32 HNE     1      23.370  17.785  -0.392  1.00  0.00
 C
HETATM   33  C33 HNE     1      24.907  17.861  -0.460  1.00  0.00
 C
HETATM   34  C34 HNE     1      25.349  19.336  -0.461  1.00  0.00
 C
HETATM   35  O35 HNE     1      -2.085  -2.760   0.479  1.00  0.00
 O
HETATM   36  C36 HNE     1      -2.528  -4.235   0.480  1.00  0.00
 C
HETATM   37  O37 HNE     1       0.634  -3.545   0.078  1.00  0.00
 O
HETATM   38  O38 HNE     1       2.561   3.347   0.017  1.00  0.00
 O
HETATM   39  C39 HNE     1       6.149   1.220   0.103  1.00  0.00
 C
HETATM   40  O40 HNE     1       8.245   2.945   0.106  1.00  0.00
 O
HETATM   41  C41 HNE     1       6.515   6.532   0.107  1.00  0.00
 C
HETATM   42  O42 HNE     1       8.550   8.079   0.107  1.00  0.00
 O
HETATM   43  C43 HNE     1      12.138   5.919   0.114  1.00  0.00
 C
HETATM   44  O44 HNE     1      13.964   7.397   0.135  1.00  0.00
 O
TER      45      HNE     1
ENDMDL
MODEL        2
HETATM    1  C1  HNE     1      29.708   0.807  -0.175  1.00  0.00
 C
HETATM    2  C2  HNE     1      30.615  -0.183   0.220  1.00  0.00
 C
HETATM    3  C3  HNE     1      30.246  -1.533   0.166  1.00  0.00
 C
HETATM    4  C4  HNE     1      28.970  -1.892  -0.282  1.00  0.00
 C
HETATM    5  C5  HNE     1      28.062  -0.902  -0.677  1.00  0.00
 C
HETATM    6  C6  HNE     1      28.431   0.447  -0.624  1.00  0.00
 C
HETATM    7  C7  HNE     1      32.020   0.212   0.713  1.00  0.00
 C
HETATM    8  H11 HNE     1      29.995   1.857  -0.134  1.00  0.00
 H
HETATM    9  H12 HNE     1      27.077  -1.179  -1.023  1.00  0.00
 H
HETATM   10  H13 HNE     1      27.731   1.211  -0.928  1.00  0.00
 H
HETATM   11  N11 HNE     1      28.564  -3.377  -0.341  1.00  0.00
 N
HETATM   12  C12 HNE     1      27.121  -3.495  -0.865  1.00  0.00
 C
HETATM   13  C13 HNE     1      26.715  -4.979  -0.924  1.00  0.00
 C
HETATM   14  N14 HNE     1      25.272  -5.097  -1.449  1.00  0.00
 N
HETATM   15  C15 HNE     1      24.866  -6.581  -1.507  1.00  0.00
 C
HETATM   16  C16 HNE     1      23.423  -6.699  -2.032  1.00  0.00
 C
HETATM   17  N17 HNE     1      23.017  -8.184  -2.090  1.00  0.00
 N
HETATM   18  C18 HNE     1      21.574  -8.301  -2.615  1.00  0.00
 C
HETATM   19  C19 HNE     1      21.168  -9.786  -2.674  1.00  0.00
 C
HETATM   20  N20 HNE     1      19.744  -9.902  -3.191  1.00  0.00
 N
HETATM   21  C24 HNE     1      22.930  -6.034  -3.330  1.00  0.00
 C
HETATM   22  O24 HNE     1      26.439  -2.604  -1.862  1.00  0.00
 O
HETATM   23  C25 HNE     1      27.681  -6.177  -0.972  1.00  0.00
 C
HETATM   24  O26 HNE     1      25.572  -7.499  -0.554  1.00  0.00
 O
HETATM   25  O26 HNE     1      20.888  -7.419  -1.615  1.00  0.00
 O
HETATM   26  C28 HNE     1      19.338 -11.387  -3.250  1.00  0.00
 C
HETATM   27  C29 HNE     1      17.895 -11.505  -3.775  1.00  0.00
 C
HETATM   28  C30 HNE     1      17.489 -12.989  -3.833  1.00  0.00
 C
HETATM   29  C31 HNE     1      16.046 -13.107  -4.358  1.00  0.00
 C
HETATM   30  C32 HNE     1      15.640 -14.591  -4.417  1.00  0.00
 C
HETATM   31  C33 HNE     1      14.197 -14.709  -4.941  1.00  0.00
 C
HETATM   32  C34 HNE     1      13.791 -16.194  -5.000  1.00  0.00
 C
HETATM   33  C35 HNE     1      12.348 -16.312  -5.524  1.00  0.00
 C
HETATM   34  C36 HNE     1      11.942 -17.796  -5.583  1.00  0.00
 C
HETATM   35  C37 HNE     1      10.499 -17.914  -6.108  1.00  0.00
 C
HETATM   36  C38 HNE     1      10.093 -19.398  -6.166  1.00  0.00
 C
HETATM   37  C39 HNE     1       8.650 -19.516  -6.691  1.00  0.00
 C
HETATM   38  C40 HNE     1       8.244 -21.001  -6.750  1.00  0.00
 C
HETATM   39  C41 HNE     1       6.801 -21.118  -7.274  1.00  0.00
 C
HETATM   40  O42 HNE     1      19.451 -11.540  -1.762  1.00  0.00
 O
HETATM   41  C41 HNE     1      21.374  -9.611  -1.158  1.00  0.00
 C
HETATM   42  O42 HNE     1      32.811  -1.057   1.082  1.00  0.00
 O
HETATM   43  C43 HNE     1      34.215  -0.662   1.575  1.00  0.00
 C
HETATM   44  O44 HNE     1      32.639   0.350  -0.646  1.00  0.00
 O
TER      45      HNE     1
ENDMDL
END
Kindly resolve my problem as soon as possible. I am waiting for your answer.


On Fri, Feb 15, 2019 at 10:47 PM suchita sakore <suchitasakore00 at gmail.com>
wrote:

> Respected sir/madam,
> I am doing a project under my post graduation.  I am doing a simulation of
> a lipid ion channel by using gromacs software. I am facing problem while
> generating the gro file. I have built peptide by using discovery studio
> software.
> while running the following command :
> gmx_mpi pdb2gmx -f pep.pdb -o pep.gro
>  The error seen is that the molecule is undefined in the PDB format. The
> gromacs software is  not able to recognize the molecule. I am attaching
> here the file on which I am working right now. Kindly resolve my problem as
> soon as possible. I am waiting for your answer.
> Thanking you in anticipation.
>
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