Dear All:<div><br></div><div><br></div><div><b><font class="Apple-style-span" color="#000099">[1 - Situation]</font></b></div><div>I am trying to define "stretch" between two bonded atoms (for example, in my system PE (polyethylene), C-C).</div>
<div><br></div><div><b><font class="Apple-style-span" color="#3333FF">[2 - ffoplsaa.rtp file]</font></b></div><div>In ffoplsaa.rtp file, I assigned </div><div> C1 > opls_136</div><div> C2 > opls_135</div>
<div>This can be done by my own idea, so it does not bother anything.</div><div>And totally okay.</div><div><br></div><div><b><font class="Apple-style-span" color="#3333FF">[3 - opls_xxx and atom type]</font></b></div><div>
I found that the oplsaa interpret those "opls_xxx" atoms to atom types (which are in ffoplsaabon.itp file) as follows,</div><div> opls_136 > CT</div><div> opls_135 > CT.</div><div><br></div>
<div><div>( from a file containing </div><div> opls_136 CT 6 12.01100 -0.120 A 3.50000e-01 2.76144e-01</div><div> opls_137 CT 6 12.01100 -0.060 A 3.50000e-01 2.76144e-01</div><div>)</div>
<div><br></div><div><font class="Apple-style-span" color="#3333FF"><b>[4 - ffoplsaabon.itp]</b></font></div><div>Based on the information in the section [2] and [3] above, I added following two sentences in the ffoplsaabon.itp file.</div>
<div><br></div><div><div> [ bondtypes ]</div><div> ; i j func b0 kb</div></div><div> CT CT 1 0.14900 334720.0 ;</div><div><br></div><div><b><font class="Apple-style-span" color="#3333FF">[5 - pdb2gmx result]</font></b></div>
<div>Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for my PE system.</div><div>After that, when I looked at the topology file (e.g. topol.top), I could not find any information in the [ bonds ] section (after the [ atoms ] section).</div>
<div>In other words, topol.top shows nothing in [ bonds ] section.</div><div> [ bonds ]</div><div> ; ai aj funct c0 c1 c2 c3</div><div> 1 2 1</div><div>
<br></div><div><b><font class="Apple-style-span" color="#3333FF">[6 - Question!]</font></b></div><div>I think my mistake came from section [3] or [4].</div><div> (1) Would you please let me know what I did wrong...?</div>
<div> (2) If someone is familiar with defining stretch, angle, dihedral and torsion in ffoplsaabon.itp, would you please give me an idea on how-to?</div><div> (3) Would you please summarize how the gromacs maps opls_xxx with atom type (C, CT... etc)?</div>
<div><br></div><div><b><font class="Apple-style-span" color="#3333FF">[7 - Thank you!]</font></b></div><div>Thank you so much your participation and help!!!</div><div><br></div><div><br></div><div>Sincerely,</div><div><br>
</div><div>Kim</div><div><br></div></div>