[gmx-users] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?

Zhang, Cheng c.zhang.11 at ucl.ac.uk
Thu May 21 11:31:59 CEST 2015

Dear GROMACS experts,

I am using pdb2gmx for a protein with 5 disulfind bond


The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a result, 10% margin of any value of the "reference length" in specbond.dat cannot cover all of the 5 Cys SG distance.

I understand that a typical disulfide bond should be about 2.05 Å in length. However, if I still want to keep them, can I change the 10% margin to a higher value (e.g. 15%)?

Thank you very much.

Yours sincerely


(Thank you for Justin's reply at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097699.html

Would it be possible if I can simply reply to you for the thread instead of creating a new one?)

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