[gmx-users] disulfide bond missing even with -ss
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
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?
Justin A. Lemkul, Ph.D.
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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