Re: [gmx-users] query about protein-ligand complex

Hi Sangeeta, Also check whether you have isolated water molecules in your system (notably the one starting at atom id 13339). If so, that may be a cause of crash and it would be better just to delete the water molecule. Best, Tsjerk On 7/3/06, Mark Abraham <[EMAIL PROTECTED]> wrote: sangeeta

Re: [gmx-users] query about protein-ligand complex

sangeeta wrote: I could not mail you as our net was down, you asked me "Is your system properly minimized? " My question is how can I understand whether my system is properly minimised? Look at the structure before you minimize it, and look at the structure after you minimize it. See what ha

Re: [gmx-users] query about protein-ligand complex

I could not mail you as our net was down, you asked me "Is your system properly minimized? " My question is how can I understand whether my system is properly minimised? the run is still going on, I can realize that something is going wrong. But I can not detect it.The log file is giving the

Re: [gmx-users] query about protein-ligand complex

On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote: > > Dear all, > > I am trying to run the dynamics of protein-ligand complex following the > tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1" > . I am running position restricted dynamics of the 91az8.pdb protein as > mentioned

[gmx-users] query about protein-ligand complex

Dear all, I am trying to run the dynamics of protein-ligand complex following the tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1" . I am running position restricted dynamics of the 91az8.pdb protein as mentioned in the tutorial trp.pdb & drg.pdb)in a Linux server machine, I c