Hello everyone,
I'm a fairly new GROMACS user. I'm running GROMACS 4.0.5 on top of Ubuntu
Linux 9.10. I am still learning a lot.
I just tried to set up my first fairly complex simulation, and it failed. I
have a protein of interest, a beta barrel with a hydrophobic, ligand-binding
interior. I am interested in making mutations to this protein, with the goal
of getting it to bind to a rather different ligand than the one it normally
binds.
The way that I propose to go about studying this problem is to construct a
partially-unfolded version of the protein structure, add my ligand of interest,
and then run an energy minimization.
My first naive attempt to construct the partially-unfolded protein was not
successful. I knew that it might have problems, but I tried it anyway. Using
Biopython, I rotated the atomic coordinates so that the beta barrel was
parallel to an axis. Then I simply pulled all of the atoms 3 Angstroms away
from the axis. Finally, I inserted my ligand. Visually, inspecting the
starting structure with PyMol, I didn't see anything egregious. However, I
could have some unwanted close contacts.
I got a few "long bond" warnings from pdb2gmx, but I persisted. I got through
genbox, editconf, and my first grompp sucessfully. But then when I tried the
first, position-restrained energy minimization, it aborted with too many LINCS
warnings. I blew the system up.
These LINCS warnings could come from close contacts, or from large forces in
over-stretched bonds which resulted from my crude approach to expanding the
protein structure. Whatever the cause, I need a smarter way to start. I am
open to ANY suggestions!
What I THINK I might want to do is to manipulate the starting structure in a
more natural way. For example, selecting some peptide bonds in the beta turns,
and changing their angles. A program which allows me to manipulate structures,
and not just simulate natural forces, is what I think I need.
Surely, people who have used GROMACS will have faced problems simliar to mine.
Thanks for your advice!
John Ladasky
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