RE: [gmx-users] Re: PBC - Protein - ligand

2011-11-09 Thread Dallas Warren
own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Steven Neumann Sent: Tuesday, 8 November 2011 8:30 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Re: PBC - Protein

Re: [gmx-users] Re: PBC - Protein - ligand

2011-11-08 Thread Steven Neumann
Thank you Justin, Mark and Tsjerk. I used the following workflow trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol trjconv -s md.tpr -f pbc_fix.xtc -n index.ndx -pbc cluster -o pbcfixcluster.xtc (Protein+ligand group) trjconv -s md.tpr -f pbcfixcluster.xtc -o center.xtc -center (center on t

Re: [gmx-users] Re: PBC - Protein - ligand

2011-11-08 Thread Steven Neumann
On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Tsjerk, >> >> Thank you. Unfortunately my ligand is not with protein. I put my ligand >> around my protein (in water) running separate simulations to see where can >> it bind. It is close to protein but no

Re: [gmx-users] Re: PBC - Protein - ligand

2011-11-07 Thread Justin A. Lemkul
Steven Neumann wrote: Hi Tsjerk, Thank you. Unfortunately my ligand is not with protein. I put my ligand around my protein (in water) running separate simulations to see where can it bind. It is close to protein but not within. Any other suggestion? I used also pbc -res so I observe my ligan

[gmx-users] Re: PBC - Protein - ligand

2011-11-07 Thread Steven Neumann
Hi Tsjerk, Thank you. Unfortunately my ligand is not with protein. I put my ligand around my protein (in water) running separate simulations to see where can it bind. It is close to protein but not within. Any other suggestion? I used also pbc -res so I observe my ligand close to protein but somet