Re: [gmx-users] non-existent angles found from trajectory g_angle

Hi, problem solved and it was a stupid mistake by me. The reference structure I used (the -s option in trjconv) had the ligand out of the active site. When I selected another reference with proper positioning of the system, everything went well. Thanks anyway! Sampo Check out these cool wo

Re: [gmx-users] non-existent angles found from trajectory g_angle

Sampo Karkola wrote: Hi Mark, visualisation of the .trr file with vmd succeeded, but the original problem remains.The -pbc cluster option did not do any better. The weird thing is that after trjconv with -pbc cluster, -center tric and -ur compact (or without the latter two) produces a traject

Re: [gmx-users] non-existent angles found from trajectory g_angle

An addition: I have another trajectory with the same enzyme but another ligand with exactly the same parameters and boxtype and simulated with the same version of Gromacs and with the same machine at the same time. With this one everything seems to work fine with g_angle and I also get correct

Re: [gmx-users] non-existent angles found from trajectory g_angle

Hi Mark, visualisation of the .trr file with vmd succeeded, but the original problem remains.The -pbc cluster option did not do any better. The weird thing is that after trjconv with -pbc cluster, -center tric and -ur compact (or without the latter two) produces a trajectory with the ligand i

Re: [gmx-users] non-existent angles found from trajectory g_angle

Sampo Karkola wrote: Dear list, I have a simulation trajectory of a CYP enzyme with a ligand in a truncated octahedron box with water and ions. The simulation went nice with stabilising backbone rmsd and potential and total energies. Now I'm interested in an angle formed by two atoms in a lig

[gmx-users] non-existent angles found from trajectory g_angle

Dear list, I have a simulation trajectory of a CYP enzyme with a ligand in a truncated octahedron box with water and ions. The simulation went nice with stabilising backbone rmsd and potential and total energies. Now I'm interested in an angle formed by two atoms in a ligand and the heme iron