[gmx-users] T->A mutation for a dimer protein

Hi All, I have a protein dimer and I want to calculate a T to A mutation free energy change using TI method. Since it is a dimer, it is very convenient (and advantageous) to mutate the T in both monomer simultaneously. Gromacs will write out dH/dl sum for the two mutations together, I think.

Re: [gmx-users] GTG to GAG with amber FF99SB force field

Hi Tsjerk, Thank you for the response. I am sorry for the bad email structure which was messed up when I copy it from microsoft word to my email editor. The error message from gromacs i think comes from the multiplicity of HA-CA-CB-OH dihedral. In amber ff99sb force field, this dihedra

[gmx-users] GTG to GAG with amber FF99SB force field

Dear Gromacs users: I use gromacs.4-5-3 to calculate the free energy changes for the GTG to GAG alchemy process, where charge annihilation is performed first followed by soft core VDW calculation. When doing the soft core VDW calculation, I see this error message ?Fatal error: [ file gtg_vdw.top