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

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 wrote: > Dear GROMACS experts, > > I am using pdb2gmx for a protein with 5 disulfind bond > > > https://copy.com/kPLlSianI4LtohNy > > > The distance

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

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