[gmx-users] problem in energy minimization
Mark.Abraham at anu.edu.au
Fri Mar 13 20:55:38 CET 2009
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 residues
> missing. I have made the topology file accordingly. But after energy
> minimization, the residues between which the portion is missing, got connected.
> 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
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.
More information about the gromacs.org_gmx-users