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

[Tsjerk Wassenaar]

Hi Cheng,

You can add another entry for a disulfide bond with a different length.

Cheers,

Tsjerk

On Thu, May 21, 2015 at 11:31 AM, Zhang, Cheng <c.zhang.11 at ucl.ac.uk> wrote:

> Dear GROMACS experts,
>
> I am using pdb2gmx for a protein with 5 disulfind bond
>
>
> https://copy.com/kPLlSianI4LtohNy
>
>
> 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
>
> Cheng
>
>
> (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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-- 
Tsjerk A. Wassenaar, Ph.D.