Re: [gmx-users] creating trajectory with ligand close to the protein

2008-02-23 Thread Tsjerk Wassenaar
Hi David, If you use a structure file (.gro/.pdb) which corresponds to the starting structure and has the protein and ligand in the right place, you can do it with trjconv -pbc nojump. Cheers, Tsjerk On Sun, Feb 24, 2008 at 4:47 AM, David Osguthorpe <[EMAIL PROTECTED]> wrote: > On Sun, Feb 24,

Re: [gmx-users] creating trajectory with ligand close to the protein

2008-02-23 Thread David Osguthorpe
On Sun, Feb 24, 2008 at 01:35:51PM +1100, Mark Abraham wrote: > > > >Ive been using trjconv but it seems to be failing for a case where the > >protein switches > >image in the trajectory but the ligand does not. > > Check out trjconv -h, and if none of the options works, please describe > why th

Re: [gmx-users] creating trajectory with ligand close to the protein

2008-02-23 Thread Mark Abraham
David Osguthorpe wrote: Hi, Can anybody tell me what is the best way to re-write a trajectory run with periodic boundary conditions such that a molecule (eg. the protein) is chosen as the reference and every other molecule in the system (eg. ligands) is transformed such that its periodic imag

[gmx-users] creating trajectory with ligand close to the protein

2008-02-23 Thread David Osguthorpe
Hi, Can anybody tell me what is the best way to re-write a trajectory run with periodic boundary conditions such that a molecule (eg. the protein) is chosen as the reference and every other molecule in the system (eg. ligands) is transformed such that its periodic image closest to the referenc