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

James Starlight jmsstarlight at gmail.com
Fri Feb 24 19:37:13 CET 2012


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 ?

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?


2012/2/24 Mark Abraham <Mark.Abraham at anu.edu.au>

>  Might work, but there are lots of steric issues and potential problems.
> Mark
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