[gmx-users] MD simulations of Tyrosinase using GROMACS

Dear GMX users, I am trying to carry out MD simulations with tyrosinase protein. Tyrosinase is a tyoe-3 copper protein. In its oxygen binding active site, the protein has two copper atoms that bind to two oxygen atoms in a peroxo configuration. Each copper is co-ordinated by three histidine residu

Re: [gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

On 4/26/12 10:23 AM, mirc...@sjtu.edu.cn wrote: Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GR

[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GROMOS force field. However, I don't know how to ma

[gmx-users] MD Simulations

Dear friends, Please read nice article on MD Simulations http://www.springerlink.com/content/6jt0843463226321/ -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Li

Re: [gmx-users] MD simulations with multiple structures

pawan raghav wrote: Dear Justin, I want to know about 1. How to run MD simulations with multiple structures? Place whatever components you need in the box with editconf, genconf, etc. and run the simulation. There's really nothing special about having more than one structure (I'm assum

Re: [gmx-users] MD simulations with multiple structures

pawan raghav skrev: Dear Justin, I want to know about 1. How to run MD simulations with multiple structures? -- Pawan This is still not very informative. Do you mean several starting structures in separate simulations? -- --- Erik Marklund, PhD s

[gmx-users] MD simulations with multiple structures

Dear Justin, I want to know about 1. How to run MD simulations with multiple structures? -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (

Re: [gmx-users] MD simulations of dipeptide in crystal lattice

List User wrote: I would like to perform MD simulations of a small molecule (dipeptide) in a crystal lattice, where I believe that lattice contacts may be important for the structure and dynamics. I assume this can be done by simulating one or more unit cells and applying periodic boundary condi

[gmx-users] MD simulations of dipeptide in crystal lattice

I would like to perform MD simulations of a small molecule (dipeptide) in a crystal lattice, where I believe that lattice contacts may be important for the structure and dynamics. I assume this can be done by simulating one or more unit cells and applying periodic boundary conditions, but I don't