Re: [gmx-users] situation where ligand is connected to amino acid

On 1/2/18 9:40 PM, Zheng Ruan wrote: Hi Ming and Justin, I have the same situation in which my protein has a cysteine residue covalently linked to a drug. I'm regularly using amber99sb-ildn force field. Is there existing tools that can help parameterize the modified residue? Thank you! Sure,

Re: [gmx-users] situation where ligand is connected to amino acid

Hi Ming and Justin, I have the same situation in which my protein has a cysteine residue covalently linked to a drug. I'm regularly using amber99sb-ildn force field. Is there existing tools that can help parameterize the modified residue? Thank you! Ruan On Tue, Jan 2, 2018 at 8:04 PM, Justin Le

Re: [gmx-users] situation where ligand is connected to amino acid

On 1/2/18 2:59 PM, MD wrote: Hi Gromacs folks, I want to simulation a protein complexed with a ligand. However, the protein covalently bonded with the ligand via N-C bond. The ligand has a size of 27 atoms. The solution I could think of now is to create a modified amino acid which includes bot

[gmx-users] situation where ligand is connected to amino acid

Hi Gromacs folks, I want to simulation a protein complexed with a ligand. However, the protein covalently bonded with the ligand via N-C bond. The ligand has a size of 27 atoms. The solution I could think of now is to create a modified amino acid which includes both the amino acid side chain and t