[gmx-developers] using replace/delete syntax of termini database for specbond

Roland Schulz roland at utk.edu
Wed Aug 25 01:44:07 CEST 2010


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.

As an example: Instead of fully specifying the CYS2 it would be nice to be
able to say:
[ CYS2 ]
[ replace ]
    CB    opls_214    12.011 0.0975
    SG    opls_203   32.06500 -0.2175
[ delete ]

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.

Would this be something easy and useful to add to pdb2gmx?


ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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