Hello All,
*(all these are done in solvated medium i.e no vacuum condition)*
I have two systems
i) modeled protein and
ii) one protein-drug complex
I want to use the amber dynamics simulation studies to do analysis of
protein to check if the modeled structure/conformation is correct or not
and to check if drug is bound to the protein after running the simulations
for 10ns or long.
Please suggest me if :
1. I should use the same minimization, heating and production for both the
systems.
2. Is it necessary to include equilibration step after heating, if so why?
3. Also I have analyzed the mdcrd file of production till 2ns, it is
showing the pressure varying but I have used the NTP ensemble production
input file . What could be the possible reason for it?
4. Is it always advisable to heat the solvent first and then slowly heating
up the protein? or we can heat the solvated protein simultaneously along
with the solvent at the start without restraints.
Thanks and Regards,
Ruchika
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 06 2015 - 05:30:04 PST
