[gmx-users] disulfide bridges

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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