[gmx-users] g_helix not recognizing protein backbone

I am running g_helix on a run involving a 37 residue protein in the charmm force field. It has two long alpha helical segments. I have tried running g_helix with many different variations of commands and getting rid of PBC effects, but I always get the same error: Checking group System There are

[gmx-users] Re: g_helix not recognizing protein backbone

It worked! Thanks a lot, it was just changing HN to H in the itp file and re-running grompp to make a new tpr file. Thanks a lot. -- View this message in context: http://gromacs.5086.n6.nabble.com/g-helix-not-recognizing-protein-backbone-tp4560173p4560255.html Sent from the GROMACS Users Forum

[gmx-users] Re: Test particle insertion extra coordinate

If no one knows this, does anyone know the best way to add a coordinate to a trajectory in general? -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546083.html Sent from the GROMACS Users Forum mailing list archive at

[gmx-users] Re: Test particle insertion extra coordinate

Thanks a lot for the reply! I did as you said. I had a coordinate file where I wanted to add insert a water molecule withing a cavity. I added these lines to the .gro file: 340SOL OW 1274 2.925 0.061 2.677 0.2533 -0.1222 0.1294 340SOLHW1 1275 2.893 0.000 2.605 -0.1856

[gmx-users] Re: Test particle insertion extra coordinate

Thank you so much for taking the time to look at the code. That should work, I will try it. -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546442.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

[gmx-users] Test particle insertion extra coordinate

Hi everyone. I am trying to do test particle insertion in a cavity with the tpic option. The manual says that the trajectory file should have one extra coordinate for the cavity location. I have a trajectory from an md run that I would like to use. How do I get the extra coordinate in there, and

[gmx-users] g_wham with cylinder geometry

Hi everyone. I ran an umbrella sampling simulation of a protein in a membrane. I used pull_geometry=cylinder. I tried to analyze the results with g_wham. I got this error: Fatal error: With pull geometry 'cylinder', expected pulling in Z direction only. However, found dimensions [Y Y Y] The