Hi there<div><br></div><div>This is maybe an old question. I want to ask a general procedure of generate topology file with gromo96 force field by Dundee Prodrg. Take SDS for an example, I want to use gromos96 G45a3 forcefield. After the file is generated by dundee, I compare the forcefield parameter of G45a3 with what Dundee output for(bond length, angle, dihedral, imp, potential). There are some differences (see below). While from papers author usually just mentioned that the file is generated by Prodrg without detailed information. According to Dundee website, the forcefield is gromos which is outdated. Should I change all the forcefield parameter by hand for any molecule I want to use with gromos ff. Or there is any shortcut I can try. I understand that charge calculated by prodrg is inaccurate.</div>
<div>Additional question, would G53a6 is basically better than G45a3 for SDS?</div><div><span class="Apple-style-span" style="font-size: medium; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-size: medium; border-collapse: collapse; "><br>
</span></div><div> <span class="Apple-style-span" style="font-size: medium; border-collapse: collapse; "> DundeePRo ff45a3</span></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-size: medium;"><div>
Length Potential Length Potential</div><div>CHn-CHn 0.153 3.35E+05 0.153 7.15E+06 </div><div>C-SO1 0.143 2.51E+05 0.143 8.18E+06</div><div>SO1-S 0.143 3.35E+05 </div>
<div>S-SO2 0.143 3.35E+05 </div><div>S=SO3 0.15 3.77E+05 0.15 8.37E+06</div><div>S=SO4 0.15 3.77E+05 0.15 8.37E+06</div><div><br></div><div> angle Potential angle Potential </div>
<div>C-C-C 111 460.2 111 530</div><div>C-C-SO1 109.5 460.2 109.5 520</div><div>C-SO1-S 120 397.5 </div><div>SO1-S-SOn 109.5 460.2</div><div><br></div>
<div><br></div><div> dihedral Potential dihedral Potential</div><div>S-SO1-SO3-SO2 35.3 836.8 35.3 334.8</div><div>C-C-C-C 0 5.9 3 </div><div>SO1-C-C-C 0 5.9 3 </div>
<div>S-SO1-C1-C2 0 3.8 3 0 1.3 3</div><div>C1-SO1-S-SO4 0 1.3 3</div><div>~ </div></span>
</div><div>Mainly the potential is different. And I didnot find the exact value on the blank parts in ff45a3 categories. </div><div><br></div><div>File generated by Dundee:</div><div><br></div><div><div>[ bonds ]</div><div>
; ai aj fu c0, c1, ...</div><div> 1 2 2 0.153 334720.0 0.153 334720.0 ; C12 C11</div><div> 2 3 2 0.153 334720.0 0.153 334720.0 ; C11 C10</div><div> 3 4 2 0.153 334720.0 0.153 334720.0 ; C10 C9</div>
<div> 4 5 2 0.153 334720.0 0.153 334720.0 ; C9 C8</div><div> 5 6 2 0.153 334720.0 0.153 334720.0 ; C8 C7</div><div> 6 7 2 0.153 334720.0 0.153 334720.0 ; C7 C6</div>
<div> 7 8 2 0.153 334720.0 0.153 334720.0 ; C6 C5</div><div> 8 9 2 0.153 334720.0 0.153 334720.0 ; C5 C4</div><div> 9 10 2 0.153 334720.0 0.153 334720.0 ; C4 C3</div>
<div> 10 11 2 0.153 334720.0 0.153 334720.0 ; C3 C2</div><div> 11 12 2 0.153 334720.0 0.153 334720.0 ; C2 C1</div><div> 12 13 2 0.143 251040.0 0.143 251040.0 ; C1 SO1</div>
<div> 13 14 2 0.143 334720.0 0.143 334720.0 ; SO1 S</div><div> 14 15 2 0.143 334720.0 0.143 334720.0 ; S SO2</div><div> 14 16 2 0.150 376560.0 0.150 376560.0 ; S SO3</div>
<div> 14 17 2 0.150 376560.0 0.150 376560.0 ; S SO4</div><div><br></div><div>[ pairs ]</div><div>; ai aj fu c0, c1, ...</div><div> 1 4 1 ; C12 C9</div>
<div> 2 5 1 ; C11 C8</div><div> 3 6 1 ; C10 C7</div><div> 4 7 1 ; C9 C6</div>
<div> 5 8 1 ; C8 C5</div><div> 6 9 1 ; C7 C4</div><div> 7 10 1 ; C6 C3</div>
<div> 8 11 1 ; C5 C2</div><div> 9 12 1 ; C4 C1</div><div> 10 13 1 ; C3 SO1</div>
<div> 11 14 1 ; C2 S</div><div> 12 15 1 ; C1 SO2</div><div> 12 16 1 ; C1 SO3</div>
<div> 12 17 1 ; C1 SO4</div><div><br></div><div>[ angles ]</div><div>; ai aj ak fu c0, c1, ...</div><div> 1 2 3 1 111.0 460.2 111.0 460.2 ; C12 C11 C10</div>
<div> 2 3 4 1 111.0 460.2 111.0 460.2 ; C11 C10 C9</div><div> 3 4 5 1 111.0 460.2 111.0 460.2 ; C10 C9 C8</div><div> 4 5 6 1 111.0 460.2 111.0 460.2 ; C9 C8 C7</div>
<div> 5 6 7 1 111.0 460.2 111.0 460.2 ; C8 C7 C6</div><div> 6 7 8 1 111.0 460.2 111.0 460.2 ; C7 C6 C5</div><div> 7 8 9 1 111.0 460.2 111.0 460.2 ; C6 C5 C4</div>
<div> 8 9 10 1 111.0 460.2 111.0 460.2 ; C5 C4 C3</div><div> 9 10 11 1 111.0 460.2 111.0 460.2 ; C4 C3 C2</div><div> 10 11 12 1 111.0 460.2 111.0 460.2 ; C3 C2 C1</div>
<div> 11 12 13 1 109.5 460.2 109.5 460.2 ; C2 C1 SO1</div><div> 12 13 14 1 120.0 397.5 120.0 397.5 ; C1 SO1 S</div><div> 13 14 15 1 109.5 460.2 109.5 460.2 ; SO1 S SO2</div>
<div> 13 14 16 1 109.5 460.2 109.5 460.2 ; SO1 S SO3</div><div> 13 14 17 1 109.5 460.2 109.5 460.2 ; SO1 S SO4</div><div> 15 14 16 1 109.5 460.2 109.5 460.2 ; SO2 S SO3</div>
<div> 15 14 17 1 109.5 460.2 109.5 460.2 ; SO2 S SO4</div><div> 16 14 17 1 109.5 460.2 109.5 460.2 ; SO3 S SO4</div><div><br></div><div>[ dihedrals ]</div><div>; ai aj ak al fu c0, c1, m, ...</div>
<div> 14 13 16 15 2 35.3 836.8 35.3 836.8 ; imp S SO1 SO3 SO2</div><div> 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C10 C11 C12</div><div> 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih C8 C9 C10 C11</div>
<div> 6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih C7 C8 C9 C10</div><div> 7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih C6 C7 C8 C9</div><div> 8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C5 C6 C7 C8</div>
<div> 9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C4 C5 C6 C7</div><div> 10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih C3 C4 C5 C6</div><div> 11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C2 C3 C4 C5</div>
</div><div><div>12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C1 C2 C3 C4</div><div> 13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih SO1 C1 C2 C3</div><div> 14 13 12 11 1 0.0 3.8 3 0.0 3.8 3 ; dih S SO1 C1 C2</div>
<div> 12 13 14 17 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 SO1 S SO4</div></div><div><br></div><div><br></div><div>Thank you for your time!</div><div><br></div><div>Best!</div><div>Xueming</div><div><br></div>
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