Re: [gmx-users] ligand falling out of active site during EM

Hi, Maybe as a note for any interested but unaware. In gromacs, the middle of the box is always the middle of the *rectangular* box defined by the first three numbers in the last line of the .gro file. Cheers, Tsjerk On 5/9/06, Anton Feenstra <[EMAIL PROTECTED]> wrote: Diane Fournier wrote:> Than

Re: [gmx-users] ligand falling out of active site during EM

Diane Fournier wrote: Thank you ! I think the problem was indeed with building the box, because I redid the whole sequence on my drug-enzyme system (building the box with editconf, putting the water with genbox, and then writing my .tpr file with grompp) and ran the same (test) position restra

RE: [gmx-users] ligand falling out of active site during EM

time, the ligand was inside. Will try minimisation again. Diane -Original Message- From: [EMAIL PROTECTED] on behalf of David Mobley Sent: Mon 5/8/2006 12:22 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] ligand falling out of active site during EM Diane, On 5/8/06

Re: [gmx-users] ligand falling out of active site during EM

binding site. David -Original Message- From: [EMAIL PROTECTED] on behalf of Diane Fournier Sent: Fri 5/5/2006 3:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] ligand falling out of active site during EM Hello ! I'm trying to run a molecular dynamics on a drug-enzyme complex. I did Joh

RE: [gmx-users] ligand falling out of active site during EM

if my input coordinates have the ligand inside. What is happening ?? -Original Message- From: [EMAIL PROTECTED] on behalf of Diane Fournier Sent: Fri 5/5/2006 3:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] ligand falling out of active site during EM Hello ! I'm trying to

Re: [gmx-users] ligand falling out of active site during EM

Hi, I'm trying to run a molecular dynamics on a drug-enzyme complex. I did John Kerrigan's tutorial and everything worked fine. Now I'm trying with my system but I get a problem : the ligand keeps falling out of the active site during EM. I thought maybe it was a pbc problem and used comm-grps =

[gmx-users] ligand falling out of active site during EM

Title: ligand falling out of active site during EM Hello ! I'm trying to run a molecular dynamics on a drug-enzyme complex. I did John Kerrigan's tutorial and everything worked fine. Now I'm trying with my system but I get a problem : the ligand keeps falling out of the active site during EM