Re: Error in Minimization

From: Roman Petrenko (
Date: Tue Nov 10 2009 - 14:00:53 CST

Dear Ale,
by freezing parts of the system Axel meant that you fix certain atoms
and let others relax. Also, i think it's a general problem inserting
protein into membrane is not an easy task. I remember struggling a
couple of days with my system (dna+protein+lipids+ions+water) to get
it running.

Just proceed step by step: if you said protein is minimized (no atom
overalps), then keep it always fixed and minimize lipids only. Once
you get protein+lipids minimized, add water and ions.

Also, make sure that your periodic box is correct. Imagine your system
is span between -100 and 100 A in x direction, and if you have
periodic box with less than 200 A length in x-direction, obviously
many atoms overlap between central cell and image.

On Mon, Nov 9, 2009 at 10:19 PM, Ale Gomez <> wrote:
> Thanks Axel for your great answer.
> I am not sure about the "complex protocol" that you told me. My first step
> was keeping protein fix and then try to minimize the system but I had the
> same values. Then I fixed the membrane and ran minimize, but still doesn't
> work. Perhaps my system is too complex for this procedure that I must do
> something else??? If I am right, could you explain me what exactly should I
> do??
> When I prepared my system, I visualized it with VMD and seems like there is
> not overlapping at all. What you think must be a correct separation for my
> protein in the membrane??, now I set up it with 9 angstroms.
> Thanks in advance for all your help.
> -------------------------------------------------------------------
> Ale Gomez
> Biophysics and Molecular Modelling Group
> Physics Department
> Escuela Politecnica Nacional, Quito-Ecuador
> Ladron de Guevara E11-253.
> Phone: 593-95292408

Roman Petrenko
Physics Department
University of Cincinnati

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:29 CST