[AMBER] bond connections

From: mohammad r <mohammad.r0325.yahoo.com>
Date: Thu, 3 Dec 2015 07:02:03 +0000 (UTC)

Hi everybody,

As I am new to the amber, I want to know that when I’mgenerating my system, is it necessary to define all the bonds between atoms andmolecule? Actually my system is consisted of a protein and some lipids(whichthe pdb file is generated by packmol) and then it is solvated in water (inambertools) and neutralizing the system(by addionsrand command). I just definethe forcefield and libraries for protein, water and lipids then load the pdbfile and solvated it in water and finally save the topology and coordinatefiles. But when I start running the MD I think the bonds are messed. There issomething wrong with the internal bonded interactions.

Thank you, Mohammad

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Received on Wed Dec 02 2015 - 23:30:05 PST
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