VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Aug 27 2013 - 05:24:23 CDT

Hi
I am trying to reinsert into a 450 residue proteins a modeled (parallel
tempering) piece. As molefacture is limited to 200 atoms, I used it for
some four residue around the two to combine. Made bond by raising its
order, requested modification of the parent file. OK the bond formed
correctly, reestablishing the apha helix conformation, howeverr, one of the
bonds at the extreme of the piece subjected to molefacture was no more
bonded. The, i made this lacking bond in molefacture by the same "strategy"
above. The bond was formed but again, one of the bonds of the piece edited
was lacking. and so on, failure of making one bond is displaced along the
proteins.

Same problem if the piece subjected to molefacture is saved and then
manually inserted into the protein.

Is that a feature intrinsic to molefacture or am I doing something wrong?
Or is it a turnaround possible, for example with pfsgen?

thanks

francesco pietra