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

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Tue Jan 26 22:09:47 CET 2010

So, what EXACTLY are you doing?


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at 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


HI Tsjerk,
Thanks for your reply. But, I can't see if it is going suddenly or
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.


2010/1/25 Tsjerk Wassenaar <tsjerkw at gmail.com>

Hi Vivek,

> Now when I am processing the modified .gro file to generate box, the
> 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.


Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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