To whom this concerns,
I am going to be running a classical MD simulation using Amber ff14SB and part of my system involved an ATP. When I searched for parameters for ATP, I found a previous post (
http://archive.ambermd.org/201001/0499.html) recommending these parameters:
http://research.bmh.manchester.ac.uk/bryce/amber When I compared these parameters to ff14SB, there are some difference in the overlap for the P-OS-P angle and the torsions. I want to make sure that I do not accidentally overwrite my parameters for the protein and DNA in my system.
Do you recommend that I use these parameters from this 2003 paper with ff14SB? Is there anything that I should be aware of, because these parameters were created to be used with ff94/ff99? Is there a different method that I should go about for parameterizing ATP, so it is consistent with the ff14SB force field?
Thank you for your time and help,
David Stevens
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Received on Wed Nov 16 2016 - 14:00:03 PST
