[gmx-users] Energy minimization of crystal structure with water

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 18 07:03:07 CET 2012

On 18/03/2012 1:01 PM, NG HUI WEN wrote:
> Hi all,
> I have a seemingly simple task that turned quite tricky here.
> I am trying to perform energy minimization on a crystal structure 
> after adding hydrogen to the protein using pdb2gmx (OPLS).
> The problem I am facing now is that after energy minimization, the 
> protein and water (originally in the protein cavity) were found in 
> completely different coordinate space. Using "pbc box" in VMD, I found 
> that the water was found roughly at the original space but not the 
> protein.
> I have tried (all turned out futile)
> 1) EM with and without pbc
> 2) position restraint the protein backbone and water
> Would someone be able to help me on this? I know I must have done 
> something silly here.

This is normal. See 

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