[gmx-users] Thioester bond problem

Dear Gromacs users, I'm attempting to simulate a system composed of two proteins containing a thioester bond between the C-terminus of chain A and a cysteine residue from chain B. I wonder if the parameters for this bond to be included in the .top file exist. Also, I am having troubles figuring

Re: [gmx-users] Thioester bond problem

alberto arrigoni wrote: Dear Gromacs users, I'm attempting to simulate a system composed of two proteins containing a thioester bond between the C-terminus of chain A and a cysteine residue from chain B. I wonder if the parameters for this bond to be included in the .top file exist. Also, I

Re: [gmx-users] Thioester bond problem

Hi Alberto, I used a stupid method to deal with this kind of non-standard moiety. You can use AmberTools to parameterize your thioester, together with your proteins, and then use acpype to convert they topology and coordinate files to gromacs format. But I am not sure if you want to use amber