Others can give more specific advice on the cross-talk between the
different DNA models (i.e. BSC1) that have been produced most
recently--seek out someone from the Cheatham lab. In terms of deriving
parameters specifically for ATP, my feeling is that it'd be hard (highly
charged molecule, fairly big, with no obvious ways to cut it apart and yet
maintain the chemical character surrounding all of its flexible
components). Also remember that any parameters which are compatible with
ff99SB or other force fields taking the Cornell charge set will be expected
to be compatible with ff14SB.
Short of better advice from the Cheatham group, my suggestion would be to
take Richard Bryce's archived parameter set for ATP (he's also go lots of
other nucleotides):
http://research.bmh.manchester.ac.uk/bryce/amber
Dave
On Wed, Nov 16, 2016 at 4:57 PM, Stevens, David Ryan <drsteve2.illinois.edu>
wrote:
> 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 - 14:30:02 PST
