From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Thu Nov 20 2014 - 10:46:35 CST
Thanks, Giacomo. Good to know.
DNA NBFIX parameters were published by the Aksimentiev group
(dx.doi.org/10.1021/jz201501a), although I'm not sure how they relate
to the Venable et al. parameters.
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Thu, Nov 20, 2014 at 10:05 AM, Giacomo Fiorin
<giacomo.fiorin_at_gmail.com> wrote:
> Hi Jeff, my colleagues and I just used this NBFIX on a J Chem Phys paper
> that should be out in a few days. The systems were multilamellar stacks of
> saturated fatty acids at varying ratios between protonated and unprotonated
> carboxyl groups. The distribution of Na+ ions behaved fairly regularly
> across very different protonation states (pH levels?), giving always a
> stable equilibrium between adsorbed and solvated ions.
>
> So I don't know about acidic proteins, but I can say that it does seem to
> behave consistently also on systems less charged than phospholipid bilayers.
>
> DNA may still need to be treated specifically?
>
> Giacomo
>
> On Thu, Nov 20, 2014 at 10:18 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>>
>> Dear NAMD users,
>>
>> I've noticed that the CHARMM force field distribution contains the
>> NBFIX parameters for Na+ ions and carboxylate oxygen atoms for
>> non-lipid systems:
>>
>> SOD OC -0.07502 3.23 ! For prot carboxylate groups
>> SOD OC2D2 -0.07502 3.23 ! For carb carboxylate groups
>> SOD OG2D2 -0.07502 3.23 ! For CGenFF carboxylate groups
>>
>> The paper (dx.doi.org/10.1021/jp401512z) in which these NBFIX
>> parameters were given was about lipids, but in the last line the
>> authors say:
>>
>> "Likewise, the NBFIX values obtained here could be applied
>> to other biopolymers but also require validation. The
>> environment on a membrane surface differs from that of a
>> protein or DNA."
>>
>> Are people using these NBFIXes for proteins? With CGenFF? Has the
>> validation mentioned in the paper been done by anyone? Are people just
>> assuming using the NBFIX is as good or better than not using it? I'm
>> inclined to do the latter.
>>
>> Thanks,
>> Jeff
>>
>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
> https://icms.cst.temple.edu/members.html
> http://giacomofiorin.github.io/
>
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