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

[Shine Devaraj]

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.

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.

Thanks in advance,

-Shine











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Shine Devaraj
Assistant Professor
Department of Biotechnology & Bioinformatics
Dr. D Y Patil University, Navi Mumbai
Associate Staff
University of Central Lencashire, Preston, UK
E:Mail: shinedevraj at dypatil.edu,shine_d at rediffmail.com
Contact: (0)9320368486
Off: 022-39286142