Re: [gmx-users] Simulation of the protein-ligand system embedded in membrane

2012-07-26 Thread James Starlight
Mark, > Only if the apo form has room for you to cut and paste in all your > ligands... You'll have to equilibrate independently in each case, so you > don't gain anything by not creating the system from the beginning each time. This can gain in terms of avoiding of time-consumptions solvation

Re: [gmx-users] Simulation of the protein-ligand system embedded in membrane

2012-07-26 Thread Mark Abraham
On 26/07/2012 10:14 PM, James Starlight wrote: Dear Gromac's users! I have some questions about simulation of the membrane protein complexed with it's ligand in the membrane environment. 1- I want to simulate number of such similar systems ( e.g protein in POPC bilayer) which differs only in l

[gmx-users] Simulation of the protein-ligand system embedded in membrane

2012-07-26 Thread James Starlight
Dear Gromac's users! I have some questions about simulation of the membrane protein complexed with it's ligand in the membrane environment. 1- I want to simulate number of such similar systems ( e.g protein in POPC bilayer) which differs only in ligand complexed into protein interiour. Should I