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
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
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