Hi,<div><br></div><div>it would be very nice if it would be possible to use the replace/delete/add features of the termini (tdb) files also in combination with specbond. This would make it simpler to specify some non-standard linkages. </div>
<div><br></div><div>As an example: Instead of fully specifying the CYS2 it would be nice to be able to say:</div><div>[ CYS2 ]</div><div>[ replace ]</div><div><div> CB opls_214 12.011 0.0975 </div></div><div>
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SG opls_203 32.06500 -0.2175 </div></div><div>[ delete ]</div><div><div> HG </div></div><div><br></div><div>For this example the saving would be very limited. But with a large number of possible linkages this would give a considerable saving in specifying the topology for possible combinations of linkages. The residue used as basis (CYS) for the modified residue (CYS2) could come from the beginning of the name or could be specified explicitly. This modified residue could be used by a specbond line (which wouldn't change from the current line using CYS2). It seems this feature could be implemented by a very limited patch because it would use only features already implemented for termini. But I don't understand the termini code so I can't judge this myself. Also I'm not sure whether it might be a problem with the charge groups.</div>
<div><br></div><div>Would this be something easy and useful to add to pdb2gmx?</div><div><br></div><div>Roland</div><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>