[gmx-users] disulfide bond missing even with -ss

Justin Lemkul jalemkul at vt.edu
Sun Jan 21 16:37:32 CET 2018

On 1/21/18 10:29 AM, MD wrote:
> I modified the specbond.dat and change the cutoff to be 2.04A, still
> nothing...

Please don't spam the list with minute-by-minute updates.

Provide your pdb2gmx command, full screen output, and whatever evidence 
you have that the bond wasn't formed. The definitive answer is in your 
topology. If it's not there, we can diagnose.


> On Sun, Jan 21, 2018 at 10:23 AM, MD <refmac5 at gmail.com> wrote:
>> I have also tried renaming my two CYS to be CYS2 but no luck either.
>> On Sun, Jan 21, 2018 at 10:22 AM, MD <refmac5 at gmail.com> wrote:
>>> gromacs did ask me to confirm linking the two cys before the run, but I
>>> didn't see any log saying the bond is formed.
>>> On Sun, Jan 21, 2018 at 10:19 AM, MD <refmac5 at gmail.com> wrote:
>>>> Hi Gromacs folks,
>>>> I realized I kept losing disulfide bond after gmx. The length is 2.01A
>>>> but I did use -ss when pdb2gmx. Any thoughts?
>>>> Thanks,
>>>> Ming


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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