[AMBER] internal geometry restraint

From: Jio M <jiomm.yahoo.com>
Date: Tue, 26 Nov 2013 08:06:20 -0800 (PST)

Dear All

I have three linear polymers and I have placed them parallel to each other. I am not sure they have been placed 'very close' because my script just considered the atoms as point coordinates while placing them. So when I run a simulation they are repelled to each other in just 50 ps and the internal geometry of each polymer chain is destroyed badly.
What I am thinking is to run first some simulation considering three polymer chains as 'hard rods', that is keeping internal geometry coordinates of a polymer constrained (all atoms in a polymer chain being fixed with respect to each other; keeping internal geometry of polymer chain fixed) so that they just act as hard rods and can adjust their positions and later I release the restraints.

I know the positional restraints that we can keep the whole structure fixed like (with ntr =1 ). In above case which flag is to be used? NMR restraints is a good idea or something simple?

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Received on Tue Nov 26 2013 - 08:30:02 PST
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