[gmx-users] Specbond.dat file

Hemalatha Jayabal hemalathajayabal at gmail.com
Tue May 22 12:01:08 CEST 2018


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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