Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

On 05/02/10 00:43, vivek sharma wrote: Hi Mark, Thanks for your response, it worked well for few molecule but not for all. As I mentioned first I am doing docking and then processing receptor through pdb2gmx and ligand through PRODRG server. But number of Hydrogen atoms in docked ligand and PRODR

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

Hi Mark, Thanks for your response, it worked well for few molecule but not for all. As I mentioned first I am doing docking and then processing receptor through pdb2gmx and ligand through PRODRG server. But number of Hydrogen atoms in docked ligand and PRODRG generated topology are not same. Althou

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

>> ------------- > >> When the only tool you own is a hammer, every problem begins to resemble > a > >> nail. > >> > >> > >> > >> From: gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] > >

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

On 27/01/10 15:58, vivek sharma wrote: Hi Dallas, I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water media. For the same I am using PRODRG server to generate topologies for ligand molecule as gromacs can generate topology for 20 st

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

problem begins to resemble a >> nail. >> >> >> >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of vivek sharma >> Sent: Monday, 25 January 2010 7:38 PM >> To: Discussion list for GROMACS users >> Subject: Re:

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

; gmx-users-boun...@gromacs.org] *On Behalf Of *vivek sharma > *Sent:* Monday, 25 January 2010 7:38 PM > *To:* Discussion list for GROMACS users > *Subject:* Re: [gmx-users] Ligand coming out while trying Drug-enzyme > tutorial > > > > HI Tsjerk, > > Thanks for your repl

RE: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

only tool you 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 vivek sharma Sent: Monday, 25 January 2010 7:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Ligand coming out

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

HI Tsjerk, Thanks for your reply. But, I can't see if it is going suddenly or gradually. What i can see is the ligand is away from the molecule after editing the gro file with PRODRG output. It seems liek PRODRG has modified the co-ordinates that places ligand away from the protein. ~Vivek 2010/1

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

Hi Vivek, > Now when I am processing the modified .gro file to generate box, the ligand > and cofactor are going away from the protein molecule and I am not able to > analyze the complex. Gradually going away, or suddenly jumping? In the latter case, read up on periodic boundary conditions. Tsj