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

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 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


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