[gmx-users] Specbond.dat file

Hemalatha Jayabal hemalathajayabal at gmail.com
Tue May 22 09:24:47 CEST 2018

Hi all,

I have added a residue (Hydroxyproline) to my .rtp files and have updated
the hdb and ffbonded files. While browsing through the manual about
specbond.dat, it says that any "special bonds" are to be listed
specifically here. Does this mean for the newly added residue also, the
bond connections are to be added? (Irrespective of whether it is forming a
basic head to tail inter residue bonds with the other standard residues
preceding and following it). If so, is it safe to use the distance between
the atoms (that forms inter residue bonds) from protein structure and use
it in the "length" factor in specbond.dat?

Thank you all in advance

Best Regards

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