[gmx-users] Ligand-protein free binding energy is become positive

I’m using MM-PBSA on gromacs to calculate free binding energy of some ligands into K-Ras (pdb-ID: 4epy). To validate MD simulation protocol and to setup a rational threshold for evaluating the results, the co-crystal ligand was considered as the reference ligand. Results showed that free binding

[gmx-users] Umbrella sampling

Hi everybody I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything is ok but some aspects of the procedure remain a bit unclear to me. Why don’t we need to do NVT equilibration before first MD? And why pull codes are applied during NPT equilibration of selected windows or

[gmx-users] How to add a repulsive harmonic potential through define virtual atom?

Hello dear GMX users I want to predict the probability binding of ligand to protein by unguided simulation. But when I increased concentration of ligand in the simulation box, the ligands has aggregated. So I decide to add repulsive potential between some atoms of ligands. I had search the

[gmx-users] (no subject)

Hello dear friends I want to simulate a Ligand-Protein complex in GROMACS by using amber forcefield https://www.google.com/search?q=forcefieldnewwindow=1sa=Xbiw=1366bih=657tbm=ischtbo=usource=univei=WEaQVYH_AoWdsgH06q6ICgved=0CE4QsAQ and need essential MDP files. Can anyone provide me that files?