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

[Dallas B. Warren]

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
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

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

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.

Tsjerk


--
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--

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