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 <armadillocomman...@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@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-requ...@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 _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
