From: Axel Kohlmeyer (
Date: Fri Jul 19 2013 - 11:56:29 CDT

On Fri, Jul 19, 2013 at 6:01 PM, <> wrote:
> Dear All,

two remarks:

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

wouldn't it be better to post a question to namd-l instead of vmd-l if
you worry about NAMD?

> 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?

what would happen if somebody here tells you "there is no problem" and
then sometime later you find out (or somebody else tells you) that the
opposite is true? or if things are the other way around? you will have
to figure out a way to convince yourself either way.

now, if you would ask how you can determine whether you can skip those
residues or not that would be a different thing. but then again, every
system is different and thus you are in the best position to find this
out, since you know exactly what you are working on and what you are
looking for in your simulations, right?


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

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.