[gmx-users] issue regarding gromacs software
Justin Lemkul
jalemkul at vt.edu
Sat Feb 16 20:05:40 CET 2019
On 2/16/19 5:51 AM, suchita sakore wrote:
> 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.png
Again, please *copy and paste text* to report error messages. No image
comes through.
You have unnatural amino acids, so pdb2gmx won't know how to deal with
them. Force fields only account for what has been parametrized. If you
want to do something new, you need to paraemtrize the residue yourself.
This can be arduous depending on the complexity of the new residue.
-Justin
> 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 <mailto: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.
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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