AMBER Archive (2005)

Subject: AMBER: advice needed for minimization and dynamic protocol

From: chaiann ng (andy810915_at_hotmail.com)
Date: Thu Jun 02 2005 - 20:33:44 CDT

Hi Amber user

I am doing modeling using nmr data. I have the preliminary structures from
CYANA, so I do not use the nmr restrains in sander. My protocol is describe
below:
1st MINI -> 2nd MINI -> 1st DYN(20)-> 2nd DYN(20ps) -> 3rd DYN(100ps) -> 1st
MINI -> 2nd MINI

After the 3rd DYN, i output the md3.mdcrd to 500.rst for the following MINI.

My question is do i need to re-image the md3.mdcrd before output 500.rst
files for the following MINI or it does not matter the results. All of the
above is performed using explicit solvent model. I already finished the
simulation with water and chloroform. If it will make a big difference, then
I will need to consider to them again. Any advise is appreciated.

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