[gmx-users] Atoms are fused after inserting in membrane

[Justin Lemkul]

On 3/26/13 5:17 AM, Shine Devaraj wrote:
> Dear gromacs users
>
> I have prepared a complex system consists of a protein and carbohydrate in
> lipid membrane using the
> KALP-membrane tutorial. After concatenating the three coordinate files, I
> visualized
> using VMD, but around 18 lipid atoms and more than 25 water molecules are
> joined with my protein
> residues as well as carbohydrate.
>

None of these molecules are "fused," but VMD thinks bonds exist because atoms 
are close together.

> I proceed to energy minimization  and it stops after reaching a step at
> ~500, showing high energy on one atom.
>
> My question is how to rectify this. I visualized using VMD and manually
> delete fused lipid and water molecule, but it creates large volume in
> membrane. I could not move forcefully because it disturb the conformation.
>
> Is any other way to correct it before proceeding to next phase.
>

You need to prepare the system more carefully.  If you are following the 
protocol from my tutorial, then you've probably over-packed the lipids such that 
they get very close to the protein, though the outcome of the shrinking step 
energy minimizations should have made it obvious that something was wrong.  As 
for the position of the carbohydrate, that's up to you to figure out.  Water 
molecules also should not have gotten close to the protein or lipids if you use 
the approach described in the tutorial (increasing vdW radii to avoid solvation 
within the membrane).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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