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
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.
Mark
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