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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