VMD-L Mailing List

From: melis.yildirim_at_boun.edu.tr
Date: Fri Jul 19 2013 - 11:01:49 CDT

Dear All,

I want to run a NAMD simulation on two separate proteins which have 2
and 3 chains respectively.

The first protein with 2 chains, have 2 missing residues in one of the
chains and 3 in the other. The second protein has 4 missing residues
in one of its 3 chains. However all these residues are not
functionally important.

I know that modelling them is required for simulations but just to be
sure again, can I run simulations with these two systems without
modelling? Will that create a problem?

Best Regards,
Melis Yıldırım
MS Student
Bogazici University Polymer Research Center
Istanbul / Turkey