[gmx-users] Specbond.dat file

[Mark Abraham]

Hi,

This is all specified in the .rtp file, e.g. with the plus and minus
symbols on atoms in the bonds section. Look there and compare with
functioning residues.

Mark

On Tue, May 22, 2018, 12:02 Hemalatha Jayabal <hemalathajayabal at gmail.com>
wrote:

> Hi,
>
> Thank you.
>
> When I used pdb2gmx to generate the topology using CHARMM, I could see from
> the bonds section that the bonds were not created between the newly added
> residue i.e hydroxyproline and the following residue(glycine). But, I also
> noted that bonds were created between the newly added residue i.e.
> Hydroxyproline and its preceding residue (proline). I did not get any error
> about any parameter being missing. What might be the possible reason for
> such behavior? Am I missing out something in the process of addition of
> residue? (I thought not mentioning bonds in specbond.dat might be a
> probable reason)
>
> Any insight regarding this would be highly helpful.
>
> On Tue 22 May, 2018, 13:14 Paul Bauer, <paul.bauer.q at gmail.com> wrote:
>
> > 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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