[gmx-users] How to define new residue in GROMACS?

[Yiming Chen]

For example, I want to add GTP as residue current force field, and after
that pdb2gmx will be able to recognize GTP molecule.

At first, I created GTP.pdb:

REMARK   This PDB file is created by CS Chem3D

REMARK

COMPND   Untitled-1.pdb

HETATM    1  C   UNK     0      -0.561   0.002  -1.145
   C
HETATM    2  C   UNK     0       0.328  -1.116  -1.641
   C
HETATM    3  C   UNK     0       1.149  -1.405  -0.410
   C
HETATM    4  C   UNK     0       1.361   0.002   0.113
   C
HETATM    5  C   UNK     0       2.929  -0.248   3.300
   C
HETATM    6  C   UNK     0       5.299  -0.874   2.006
   C
HETATM    7  C   UNK     0       0.958   0.191   2.581
   C
HETATM    8  C   UNK     0       4.131  -0.512   4.102
   C
HETATM    9  C   UNK     0       3.049  -0.325   1.915
   C
HETATM   10  H   UNK     0       7.349  -1.394   2.036
   H
HETATM   11  H   UNK     0       6.594  -1.285   0.394
   H
HETATM   12  H   UNK     0      -1.494  -0.383  -0.678
   H
HETATM   13  H   UNK     0       0.972  -0.803  -2.494
   H
HETATM   14  H   UNK     0       0.603  -2.041   0.322
   H
HETATM   15  H   UNK     0       2.165   0.515  -0.468
   H
HETATM   16  H   UNK     0       2.947  -2.013   0.015
   H
HETATM   17  H   UNK     0       0.178  -2.926  -2.340
   H
HETATM   18  H   UNK     0      -0.106   0.431   2.504
   H
HETATM   19  H   UNK     0       6.160  -1.008   3.934
   H
HETATM   20  N   UNK     0       1.777  -0.040   1.517
   N
HETATM   21  N   UNK     0       1.651   0.064   3.691
   N
HETATM   22  N   UNK     0       4.234  -0.642   1.256
   N
HETATM   23  N   UNK     0       5.281  -0.814   3.397
   N
HETATM   24  N   UNK     0       6.507  -1.212   1.437
   N
HETATM   25  O   UNK     0       0.158   0.696  -0.141
   O
HETATM   26  O   UNK     0       2.362  -2.026  -0.746
   O
HETATM   27  O   UNK     0      -0.417  -2.236  -2.037
   O
HETATM   28  O   UNK     0       4.142  -0.481   5.335
   O
HETATM   29  O   UNK     0      -0.826   0.950  -2.157
   O
HETATM   30  O   UNK     0      -5.338   2.374  -0.127
   O-1-
HETATM   31  O   UNK     0      -3.230   0.072  -2.587
   O
HETATM   32  O   UNK     0      -2.156   1.936  -4.009
   O-1-
HETATM   33  O   UNK     0      -5.619   0.198  -1.738
   O
HETATM   34  O   UNK     0      -4.404   2.410  -2.384
   O
HETATM   35  O   UNK     0      -5.108   0.603  -4.028
   O-1-
HETATM   36  O   UNK     0      -3.544   3.985  -0.564
   O
HETATM   37  O   UNK     0      -3.027   1.592  -0.529
   O-1-
HETATM   38  O   UNK     0      -1.402  -0.335  -4.284
   O
HETATM   39  P   UNK     0      -1.939   0.652  -3.302
   P1+
HETATM   40  P   UNK     0      -4.624   0.851  -2.639
   P1+
HETATM   41  P   UNK     0      -4.060   2.614  -0.833
   P1+
END

Then I submitted GTP.pdb to
http://davapc1.bioch.dundee.ac.uk/prodrg/index.html, and obtained
DRGGMX.ITP:

I don't know how to convert .itp file to .rtp file, and how to add new
residue to current .rtp files. Could any one help me? Thank you!
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