Dear PyMol users! I'm writing of some automatic script aimed on the embedding of the receptors into the membrane consisted of the pre-equilibrated lipids as well as hole for the protein. The main issue that some of the receptors consist of the bulky PHE or TRP side chains on their surface which are overlap with the lipids so MD simulation of this system is crushed although of long minimization stage prior to it. I'll be very thankful if someone provide me with some script for PyMol or VMD for automatic detection of these problem (overlapped) locations and removing of the overlapped lipids detected within some cutoff radios of the protein.
Thanks for help, James
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