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

[Tsjerk Wassenaar]

Hi Yiming Chen,

In this case there's no need to add GTP as a building block. Have a
look at John Kerrigan's drug - enzyme tutorial to see how to include a
prodrg topology in your simulation:

http://wiki.gromacs.org/index.php/Tutorials

Also, do note the caution regarding non-standard groups in your system
(and mixing force fields):

http://wiki.gromacs.org/index.php/Parameterization

Finally, don't use the gmx force field; it's deprecated.

Cheers,

Tsjerk

On Mon, Feb 23, 2009 at 10:32 AM, Yiming Chen
<armadillocommander at gmail.com> wrote:
> 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!
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623