Can you run that same procedure without doing anything to your protein?
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of John Ladasky Sent: Friday, 19 February 2010 2:08 PM To: gmx-users@gromacs.org Subject: [gmx-users] Assembling a good simulation starting point 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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