[gmx-users] SS bond

Dear gmx users, We are trying to make an intermolecular cystine bond between two residues in a dimeric protein (S:S - dist.: 0.203). The initial pdb file should contain the SS bond. Therefore, we used the pdb2gmx -ss -merge to generate the disulfide bond. Apparently it did not form the cy

[gmx-users] ci value

Dear Gromacs users, I am trying to run a steep minimization for a protein in a system containing 15% TFE and 85% water. When I executed mdrun I obtained the following message: Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ] Please report this to the mailing list

[gmx-users] TFE solvent box

Hi all, We want to create and simulate a solvent box containing TFE. We have already generated the TFE.gro file, and by using this file we created a box containing 38 molecules of TFE (TFE_solv.gro). We created a file TFE.top including the tfe topology (using tfe.itp, provided by GROMACS)