Hej,
the specbond.dat file is for extra bonds between non-neighbouring
residues (e.g. disulphide bridges).
So if you don't need to add anything extra for your residue there if it
doesn't do anything like a disulphide would.
Cheers
Paul
On 2018-05-22 09:24, Hemalatha Jayabal wrote:
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
Hemalatha
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