[gmx-users] Specbond.dat file

Paul Bauer paul.bauer.q at gmail.com
Tue May 22 09:43:35 CEST 2018


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.



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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