[gmx-users] problem in energy minimization

Abhik Mukhopadhyay abhikuohyd at yahoo.com
Thu Apr 2 01:50:51 CEST 2009

Hi Mark 
Sorry for the delayed reply. Somehow I missed your mail that time. 
I am doing exactly what you have suggested. I am building up this missing part and then trying to run the simulation.
Again 'm sorry for this delay.
Best regards, 

Abhik Mukhopadhyay
  Departamento Química / Faculdade de Ciências e Tecnologia 
 Universidade Nova de Lisboa , 2829-516 Caparica, Portugal 

Mob. 00351912991251

--- On Fri, 3/13/09, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] problem in energy minimization
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Friday, March 13, 2009, 7:55 PM

Abhik Mukhopadhyay wrote:
> Hi Jastin
> My pdb2gmx command line is
> pdb2gmx -ignh -f xx.pdb -o xxout.pdb -p xx.top -water spce
> When I created the topology it did not create a bond between those two
residues (between which the part is missing).

The above statement seems inconsistent with the observations below.

>     > I am trying to run a simulation on a xray structure that has 15
>     missing. I have made the topology file accordingly. But after energy
>     minimization, the residues between which the portion is missing, got
>     I tried an energy minimization with all-bonds constraint, but that i
guess did
>     not do it properly.

By far the most likely reason for the residues that should be spaced by the 15
missing residues to "get connected" was that your topology had an
interaction defined.

The fact that these residues were missing from the X-ray structure doesn't
mean you should ignore their existence. Often they can be involved in useful
chemistry. I would most likely consider using some (non-GROMACS) modelling
software to "build in" such residues before attempting any MD.

There are alternatives which involve capping the pseudo-termini and possibly
using some kind of restraints, but these will be harder to defend to your
paper's audience.

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