Yun,
This probably doesn't directly answer your question, but:
With regards to only restraining heavy atoms, I would expect that most
AMBER users use SHAKE to constrain bonds containing hydrogen (and this is
even more likely during equilibration when one sometimes only desires
"quick and dirty" but stable dynamics). If that is the case, the presence
or absence of restraints on light atoms may not be that important (although
I sense that someone may correct me on this).
With regards to backbone restraints, you would have to come up with a
fancier selection for your restraint mask. I don't work with proteins, but
I think the atom names for alpha carbons are regular enough for this
purpose.
Brian
On Sat, Oct 29, 2011 at 8:04 PM, Yun Shi <yunshi09.gmail.com> wrote:
> Hello all,
>
> I am using ff99SB to model an antibody with carbohydrate ligands.
>
> When I use something like [ restraintmask=':1-500' ], all atoms within this
> 500 residues will be restrained, right?
>
> But I also heard someone only restraining the heavy atoms, or only
> restraining the backbone atoms.
>
> I wonder if this really matters for my system. As far as I know,
> equilibration is aimed at getting the temperature and pressure right,
> mainly
> for the solvent. And as long as we are going to do a 'real' MD production
> run without restraints, it should not matter too much how we restrained the
> antibody and ligands.
>
> I am not if I am right about this. Any suggestions?
>
> Thanks,
> Yun
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>
--
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Brian Radak : BioMaPS
Institute for Quantitative Biology
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Received on Mon Oct 31 2011 - 06:30:02 PDT
