Oh thank you so much, I did not know it was a reference value. Given a range of values might exist in one system I'm guessing minimization would be the only way to deal with such a situation.
Best, Miro On Sat, May 2, 2020 at 9:53 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/2/20 6:54 AM, Miro Astore wrote: > > Hi all, > > > > I'm trying to make a protein with a fair few disulfide bridges and I > > couldn't get it to work. I chose -ss yes and increased the minimum > distance > > in specbonds.dat but it doesn't seem to want to let me see all possible > > pariings. > > specbond.dat does not set minimum distances. It sets a reference value, > and a bond is only assigned if the distance in the coordinate file is > within 10% of that reference. So if you were, for example, to increase > the value from 0.2 nm (conventional) to 0.3 nm, you'll miss the > disulfides that should be formed because the new reference range is 0.27 > - 0.33 nm and anything between 0.18 - 0.22 nm will not be assigned a > disulfide linkage. > > > Any way I can nudge it in the right direction without performing a > > minimisation with restraints? > > Depends on the range of distances in your structure, but this is often > what you have to do. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.