I recommend you do one of the earlier Amber tutorials and look for the perl process_mdout.perl functionality where you can follow the rmsd of the backbone of your protein vs time. If I understand you correctly, you want to see if the conformation is stable- this is one way to do it. I very much doubt that 10ns is enough for such a question.
However, do follow one of the Amber tutorials and particularly look at
Amber Basic Tutorials - Tutorial B1 - Section 3
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| Amber Basic Tutorials - Tutorial B1 - Section 3(Note: These tutorials are meant to provideillustrative examples of how to use the AMBER software suite to carry outsimulations that can be run on a simple workst... |
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This one is very good:
Amber Basic Workshop - Tutorial 3 - Introduction
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| Amber Basic Workshop - Tutorial 3 - Introduction(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple wo... |
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and:
antechamber
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| antechamberANTECHAMBER TUTORIAL Using Antechamber to Create Leap Input Files for Simulating Sustiva (efavirenz)-RT complex using the General Amber Force Field By Ro... |
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You can look through these tutorials and get all the info you need. They are fantastic and they will explain how to properly minimize your system and much more. The fact that your pressure hasn't 'falttened out' yet seems to indicate you haven't properly minimized your system. I'd start from scratch with these and they will explain how to use restraints and much more.
Good Luck!CG
From: Ruchika Bhat <ruchikabhat31.gmail.com>
To: AMBER Mailing List <AMBER.ambermd.org>
Sent: Friday, February 6, 2015 8:03 AM
Subject: [AMBER] Query regarding Dynamics Studies
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
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Received on Fri Feb 06 2015 - 07:30:02 PST
