[gmx-users] Re: Internal water in the membrane receptor

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 25 00:18:36 CET 2012

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.


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