Re: [AMBER] about lipids retrain

From: David A Case <>
Date: Wed, 17 Aug 2016 07:48:00 -0400

On Wed, Aug 17, 2016, Albert wrote:
> Hold lipid fixed
> 10.0 ! Force constant (kcal/(mol Angstroms^2))
> RES 1 384 ! Choose residues

This will restrain all atoms in residues 1 to 384. The sander or pmemd
programs don't have any notion of what "kinds" of atoms these are (e.g.
protein, lipid, solvent, head-groups, tails, etc.) Make a pdb file using
ambpdb, and look to see what atoms are in the residues you have chosen.

Don't be afraid to experiment: run a short simulation and see what moves.


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Received on Wed Aug 17 2016 - 05:00:02 PDT
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