From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Dec 15 2014 - 15:41:22 CST
Hi Ajasja,
My best guess is to have one atom type per CA and a lot of NBFIXes.
Jerome
On 15 December 2014 at 19:08, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
wrote:
>
> Dear all,
>
> I would like to run coarse grained simulations of protein folding similar
> to Chavez et. al. <http://pubs.acs.org/doi/abs/10.1021/ja049510+> (here is
> the supplement
> <
> http://pubs.acs.org/doi/suppl/10.1021/ja049510%2B/suppl_file/ja049510%2Bsi20040602_123057.pdf
> >).
> The model is meant to study entropic barriers to protein folding (and is
> capable of predicting folding rates if the experimental melting temperature
> is known),
>
> Basically this involves taking only the C-alpha atoms from a known
> reference structure and determining the equilibrium values for bonds,
> angles and dihedral angles from the reference. Then a vdw-like potential is
> applied, that is specific for different atom pairs. Atoms that are close
> together get an attractive+repulsive part, all other pairs get only the
> repulsive part.
> [image: Inline images 1]
>
> My first thought was to have a single atom type and account for all the
> different bonds and angles using NAMD's extraBonds
> <
> http://www.ks.uiuc.edu/Research/namd/2.10b2/ug/node27.html#SECTION00086400000000000000
> >
> feature.
> But I don't see a way to have per atom pair specific vdw forces. So my
> first question is: *is there a way to have per-atom pair specific
> attractive/repulsive nonbonded potential? *(without resorting to TCLforces)
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