[gmx-users] my protein gets cut while preparing for em

[Olli Lehtonen]

On Mon, 19 Jun 2006, Guillem Plasencia wrote:

> Then i was curious and did trjconv my system (before running mdrun energy
> minimization) into a pdb, and had a look at it, and i saw my protein was
> splitted in three different molecules, one was inside the water box (but far
> away from box center, lying in touch of one of the boxes' sides) and the
> other two parts were completely outside the box.  Worst of all, they were no
> more one single peptidic chain, but separated one.

I was having somewhat similar problem recently when I had multiple
peptides in my system (I used genconf to generate them) but in the final
structure they all had the same chain identifier, so pdb2gmx thought that
I have only one long peptide in the system (with some 1 nm long bonds).

If this is the reason, one way to check how many chains there are is to
interactively choose termini groups with pdb2gmx, you should be prompted
for each peptide unit.

By the way, if it is somehow possible to tell genconf to generate repeated
units with different chain identifiers, I would be interested to know.

regards,

Olli