Re: [gmx-users] Building Topology of a Drug (using the ff of your choice)

Hi, You could use PRODRG to build an initial topology and then use the FF definition in you gromacs distribution to edit to suit. On the PRODRG website, there is a link to the top right had of the page if memory serves me correctly to a beta server that will generate topology files consistent

[gmx-users] Centering using trjconv

Hello All. I am simulating t4 lysozyme with NAG. I have added a short peptide label to lysozyme which binds calcium ions. During the simulation there is some drift. I am attempting to re-center the protein+label+NAG+Ca ion. I am using trjconv and have setup an index file that contains only these

[gmx-users] Protein-Ligand Interactions

Hi All. I wish to analyse the dynamics of t4 Lysozyme with a small peptide attached via a disulphide bond. My MD runs are fine, however I wish to add the ligand N-acetyl glucosamine (NAG) in the active site to measure some distances from the attached peptide to the NAG molecule. I have initiall