On 05/12/10 13:20, Justin A. Lemkul wrote:
ms wrote:
On 05/12/10 10:39, swagata chakraborty wrote:
I was trying to run MD simulation of my protein in DMSO. I used the
force
field ffG53a6 and did the energy minimization after solvating the
protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a
sheet.
Please suggest where I am going wrong since the structure shouldnot
change
after solvation.
You're not giving nearly enough detail (what is the dmso/water ratio?
what is your .mdp file?) etc.
In any case, it wouldn't be the first time that simulations and
experiments disagree. How do you *know* that structure shouldn't
change? Have you tried using another force field, like OPLS?
This might just be a visualization artifact, something that gets posted
here routinely. Some slight structural changes may have occurred during
EM, such that the visualization program guess sheet instead of loop.
53A6 does tend to favor extended structures, but I would only suggest
something is wrong if (1) a real simulation is conducted and the
spurious secondary structure persists and (2) real analysis is done
(like DSSP or STRIDE) to conclude the secondary structure, rather than
just looking at it, as all visualization software uses different
heuristics to assign structures. It does not make for convincing evidence.
You are absolutely right (as almost always you are!), yet more detail,
the better. I'd say that visualizing it in Pymol using the dss command
to give the DSSP assignment could help.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
