<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi, </div><div><br></div>I recently made up a topology for ADP. You can probably modify it to ATP easily. <div>I used native OPLS atom types based on the DNA parameters (<a href="http://rnp-group.genebee.msu.su/3d/ff.htm">http://rnp-group.genebee.msu.su/3d/ff.htm</a>). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHARMM.</div><div>Please let me know if you have any question, suggestion, ....</div><div><br></div><div>Cheers,</div><div>Bin</div><div><br></div><div>===============================</div><div>In the ffoplsaa.rtp file, I added:</div><div><br></div><div><div>[ ADP ]</div><div> [ atoms ]</div><div> PB opls_440 1.100 0 ;P</div><div> O1B opls_441 -0.900 1 ;O</div><div> O2B opls_441 -0.900 2 ;O</div><div> O3B opls_441 -0.900 3 ;O</div><div> PA opls_440 1.500 4 ;P</div><div> O1A opls_441 -0.820 5 ;O2</div><div> O2A opls_441 -0.820 6 ;O2</div><div> O3A opls_442 -0.740 7 ;OS</div><div> O5' opls_442 -0.620 8 ;OS</div><div> C5' opls_443 -0.080 9 ;CT</div><div> H5'' opls_444 0.090 10 ;HC</div><div> H5' opls_444 0.090 11 ;HC</div><div> C4' opls_158 0.160 12 ;CT</div><div> H4' opls_156 0.090 13 ;HC</div><div> O4' opls_180 -0.500 14 ;OS</div><div> C1' opls_158 0.160 15 ;CT</div><div> H1' opls_156 0.090 16 ;HC</div><div> N9 opls_354 -0.050 17 ;NA</div><div> C8 opls_353 0.340 18 ;CK</div><div> H8 opls_359 0.120 19 ;H5</div><div> N7 opls_352 -0.710 20 ;NB</div><div> C5 opls_350 0.280 21 ;CB</div><div> C6 opls_351 0.460 22 ;CA</div><div> N6 opls_356 -0.770 23 ;N2</div><div> H61 opls_357 0.380 24 ;H</div><div> H62 opls_358 0.380 25 ;H</div><div> N1 opls_346 -0.740 26 ;NC</div><div> C2 opls_347 0.500 27 ;CQ</div><div> H2 opls_355 0.130 28 ;H5</div><div> N3 opls_348 -0.750 29 ;NC</div><div> C4 opls_349 0.430 30 ;CB</div><div> C2' opls_158 0.140 31 ;CT</div><div> H2'' opls_156 0.090 32 ;HC</div><div> O2' opls_171 -0.660 33 ;OH</div><div> H2' opls_172 0.430 34 ;HO</div><div> C3' opls_158 0.140 35 ;CT</div><div> H3' opls_156 0.090 36 ;HC</div><div> O3' opls_171 -0.660 37 ;OS</div><div> H3T opls_172 0.430 38</div><div> [ bonds ]</div><div> PB O3A</div><div> PB O1B</div><div> PB O2B</div><div> PB O3B</div><div> O3A PA</div><div><div> PA O1A</div><div> PA O2A</div><div> PA O5'</div><div> O3' H3T</div><div> O5' C5'</div><div> C5' C4'</div><div> C4' O4'</div><div> C4' C3'</div><div> O4' C1'</div><div> C1' N9</div><div> C1' C2'</div><div> N9 C4</div><div> N9 C8</div><div> C4 N3</div><div> C2 N1</div><div> C6 N6</div><div> N6 H61</div><div> N6 H62</div><div> C6 C5</div><div> C5 N7</div><div> C2' C3'</div><div> C2' O2'</div><div> O2' H2'</div><div> C3' O3'</div><div> C1' H1'</div><div> C2' H2''</div><div> C3' H3'</div><div> C4' H4'</div><div> C5' H5'</div><div> C5' H5''</div><div> C8 H8</div><div> C2 H2</div><div> N1 C6</div><div> N3 C2</div><div> C4 C5</div><div> N7 C8</div></div></div><div>===============================</div><div><br></div><div>===============================</div><div>In the ffoplsaabon.itp file, I added:</div><div><div>; copied from ffoplsaanr</div><div>[ angletypes ]</div><div> NA CT OS 1 109.500 418.680 ; DNA DCY</div><div><br></div><div>[ dihedraltypes ]</div><div>; these are again copied from ffoplsaanr</div><div> NA C CM CT 3 30.35430 0.00000 -30.35430 0.00000 0.00000 0.00000 ; aromatic ring DNA DTH</div><div> C CM CT HC 3 -0.77874 -2.33623 0.00000 3.11498 0.00000 0.00000 ; aromatic ring DNA DTH </div><div> HC CT CT NA 3 0.97134 2.91401 0.00000 -3.88535 0.00000 0.00000 ; RNA NA CT CT OH 3 16.74720 -16.74720 0.00000 0.00000 0.00000 0.00000 ; RNA</div><div> CM NA CT OS 3 -3.14010 -3.14010 6.28020 0.00000 0.00000 0.00000 ; DNA DCY</div><div> C NA CT OS 3 -3.14010 -3.14010 6.28020 0.00000 0.00000 0.00000 ; DNA DCY</div><div> CT OS CT NA 3 -5.23350 7.32690 6.28020 -8.37360 0.00000 0.00000 ; </div><div><br></div><div>[ dihedraltypes ]</div><div>; copied from charmm</div><div> O2 P OS P 1 0.0 0.1255 3.0</div><div> O2 P OS P 1 0.0 0.4184 2.0</div><div> OS P OS P 1 0.0 0.1255 3.0</div><div> OS P OS P 1 0.0 0.1255 2.0</div><div><br></div><div>===============================</div></div><div><div><div>On Jun 22, 2010, at 5:07 AM, Efrat Noy wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div bgcolor="#ffffff"><div><font size="2" face="Arial">Hi,</font></div><div><font size="2" face="Arial"></font> </div><div><font size="2" face="Arial">Does anyone have OPLS-AA topologies for ATP?</font></div><div><font size="2" face="Arial"></font> </div><div><font size="2" face="Arial">Thanks, Efrat</font></div>--<span class="Apple-converted-space"> </span><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div></body></html>