[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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