AMBER Archive (2006)

Subject: AMBER: simulating a small chain protein in water box

From: Dave, Sonya (
Date: Wed Nov 08 2006 - 10:03:46 CST

I want to simulate the structure of a small chain of amino acids, de novo. I actually know this chain is part of an alpha helix in a larger protein. I ran the simulation, per the tutorial about TRP cage. However, the structure does not look anything like I expect. I think this is because I am running in vacuum (the original protein also looks improper simulated in vacuum). As such, I want to simulate the chain in explicit solvent. How would I go about this? Specifically,
Can I put the water box around the result of my vacuum simulation, rather then the straight chain? Would you suggest doing that?
Do I need to start from 0 K, and slowly heat up the molecule? In the vacuum simulation, the molecule was slowly heated to 300K, so do I need to do it again for water simulation?
Do I need to do all the steps as for simulating a large protein in explicit solvent? That is, first minimize the water box, then put weak restraints on the protein, then put no restraints on the protein?
How do I determine the input files, if I do need to do all those simulations? Should I use ones similar to those I used for large protein explicit simulations? Or should I use the reheating input files?
This would be the first time i'm doing a simulation without basically following some tutorial (with minor modifications).
Thank you,

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