On 11/20/17 1:09 AM, Amir Zeb wrote:
Yes Dr. Dallas,
I have gone through free energy analysis tutorial, But I'm wondering that
whether this tutorial is working for large molecule like protein or not?
Because the tutorial has explained methane only.
No, that tutorial is not relevant nor shoul
Yes Dr. Dallas,
I have gone through free energy analysis tutorial, But I'm wondering that
whether this tutorial is working for large molecule like protein or not?
Because the tutorial has explained methane only.
Your feedback will highly be appreciated.
Thanks!
Amir
On Sun, Nov 19, 2017 at 5:54
Always a good starting point
http://www.gromacs.org/Documentation/Tutorials
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
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Thanks Mark,
Depends what you mean by "stability."
Actually, I don't know the role of metal ion if it is used as co-factor by
a particular protein. I thought to do comparative analysis by MD simulation
which might predict the possible role of metal (in this case Zn^2+). Other
analysis like RMSD, R
Hi,
Depends what you mean by "stability." A well designed study could seek to
measure or estimate the difference in the free-energy of folding, but that
would probably require an infeasibly large amount of sampling, and be
highly dependent on the quality of the parameterization of the
metal-protei
Hi gromacs users,
I want to calculate the energy for comparative analysis of protein with and
without metal ion, wherein I would like to determine the influence of metal
on protein structural stability. I have used gromacs for simulation. Please
suggest me how to do this kind of analysis? Should i
