Hi Bill,
I just want to generate first structure of my system with amber and do the rest of simulation gromacs. first I thought it's because of the method of conversion but I used acpype and ParmEd for file conversion and still the problem exists.
On Thursday, December 3, 2015 11:21 AM, Bill <ross.cgl.ucsf.edu> wrote:
How did you equilibrate? Are you following a tutorial?
Bill
On 12/2/15 11:02 PM, mohammad r wrote:
> 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 Thu Dec 03 2015 - 04:30:05 PST
