Re: [gmx-users] Aligning protein in bilayer with editconf

2009-10-27 Thread sunny mishra
Put your protein file in TMDET and it will align the protein for you perpendicular to Z axis and also the protein will be at origin in that case then you can use geom_center script provided in VMD to put the lipid in the origin and move it towards the protein. Hope it helps On Tue, Oct 27, 2009 at

Re: [gmx-users] Aligning protein in bilayer with editconf

2009-10-27 Thread Justin A. Lemkul
Anirban Ghosh wrote: Hi ALL, I am facing a strange problem, while aligning a protein molecule in a lipid bilayer. I am using the center coordinates of the lipid .gro file (values in the last line of .gro) with -box option of editconf to properly align the protein with the bilayer. Now the p

[gmx-users] Aligning protein in bilayer with editconf

2009-10-27 Thread Anirban Ghosh
Hi ALL, I am facing a strange problem, while aligning a protein molecule in a lipid bilayer. I am using the center coordinates of the lipid .gro file (values in the last line of .gro) with -box option of editconf to properly align the protein with the bilayer. Now the problem is that the protein i