[gmx-users] Specbond.dat file

[Paul Bauer]

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