Which molecular dynamics package are you using?
-James Holton
MAD Scientist
On 2/28/2020 7:00 AM, Firdous Tarique wrote:
Hello everyone
I am trying to run a molecular dynamics simulation of a protein which
has a Zn atom and few phosphorylated PTMs (Thr is phosphorylated).
PTMs and Zn play es
Hi, Firdous,
Most modern force fields have a way to describe ions, small molecules or
modified residues for MD run. And they already contain description for
phosphorilated aminoacids. So you can choose whichever you want.
But it is more appropriate to ask in the specialized mailing list, like
CCPBi
Hello everyone
I am trying to run a molecular dynamics simulation of a protein which has a
Zn atom and few phosphorylated PTMs (Thr is phosphorylated). PTMs and Zn
play essential roles to maintain the structural integrity and therefore
cannot be removed rather I want to keep both of them for my ru
Yes, I was maybe too positive in my reply. Looking more closely,
classical MD may not be appropriate here. The better way is QM/MM but
that is not quick and dirty. It depends whether the main effect of the
mutations is in the geometry of the protein or in the electronic
structure of the metal bindi
Just a word of warning regarding metals in macromolecular simulation.
There is no 'good' way of modeling protein-metal interactions in many
cases. Some metal ions are very polarizable (Ca 2+ being one example)
and the simple mechanics used in protein simulation don't allow for
this. Even using a po
GROMACS binaries are available for Macs
http://www.gromacs.org/content/view/32/100/
Afaic, GROMACS is user-friendly. There are good tutorials, and there is
even third-party GUI:
http://resal.atspace.com/grogui.htm
IMHO, the GUI is not much better than running Gromacs jobs from command
line, bu
Gromacs www.gromacs.org
It is GPL. It can certainly handle metals, although as is always the
case, you have to be careful in the choice of force field. It is fairly
user friendly (by the standards of that field ;-). Not sure what the
situation is for Macs but certainly runs well on Linux.
Alter
Hi everyone.
I have a slightly off topic question I hope someone can help with.
I have a structure of a wild type domain, which binds metal ions.
Certain mutations in chelating residues cause changes in the apparent
affinity for said metal ions.
As I have (so far) failed to crystallise the mutan
