VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Nov 14 2007 - 12:05:12 CST

I am in a silly loop, trying to merge protein and POPC membrane and removing
superimposition.

I created a 100x100A POPC (less is not enough for my protein) and inserted and
centered the protein.

Saved protein_aligned.pdb. fed to the working directory both scripts
combine.tcl and top_all27_prot_lipid.inp.

The, at

vmd -dispdev text < combine.tcl |tee combine.log

the error was:

There is no 'top' molecule in atom select's 'molId' (VMD 1.8.6).

After resetpsf, I tried various (clearly faulty) selections with no success.

Thanks for helping
francesco pietra

Incidentally, does 10x100 cause steric clashes?

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