On 25/02/2012 5:37 AM, James Starlight wrote:
Mark,
So as I understood the ussage of X-ray structure as the starting model
where the internal water is already present might be good in case to
avoid those sterric issues doesn't it ?
Yes. This was one of the options I suggested earlier.
What are additional options should I use for preparation of such
system with pdb2gmx ? Should I use posres on the internal water ( e.g
on oxygen atoms) during energy minimisation and equilibration phases?
You probably do want a contiguous block of atoms with position
restraints. That will require you have two different [moleculetype]
sections for the different "kinds" of water, since the
[position_restraints] section applies to all instances of its
[moleculetype], and you will need to disable [settle] for at least one
of those. It might be easier not to use separate restraints for a subset
of water.
Mark
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