AMBER Archive (2005)

Subject: Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied

From: pl (ladam_at_smbh.univ-paris13.fr)
Date: Tue Jan 04 2005 - 07:25:39 CST

Dear David,
That's what I started to think but as I considerably raised
the force constants I expected the backbone to move at least
a bit. I'll try some dynamics and keep you informed.
Thanks again.

> the restraints look ike they ARE working. after step 1000 when you >
> change
> the force constant, the restraint energy is ~200 kcal/mol.
> you might just be in a local minimum for the backone - minimization
> won't change the backbone in that case even in you apply restraints
> to try to bring it to another conformation. you might want to try doing
> some dynamics with the restraints. several books (like Molecular Modeling by
> Andrew Leach) have a good discussion of the limitations of local
> minimization.
>
>
> pl wrote:
>
> >Dear David,
> >
> >
> >>On Mon, Jan 03, 2005, pl wrote:
> >>
> >>
> >>
> >>>Strangely the dihedral restraints do not seem to work at all...
> >>>
> >>>
> >>You will have to explain what you mean by "do not seem to work at all".
> >>Without knowing any symptoms, no one will probably be able to offer much
> >>advice.
> >>
> >>
> >At start my dna is far from canonical B form (the backbone particularly
> >displays inflections due to some previous HBonds restraints I imposed)
> >Now I want to bring back the backbone to a B-form by forcing
> >Alpha, beta and so on to canonical values.
> >What I meant is that even after a lot of minimisation iterations, the
> >backbone did not improve at all just as if dihedral constraints were
> >not applied. In other words, the starting and resulting
> >structures superimpose almost totally.
> >One thing I noticed is that my pdb file contains * instead of ' for
> >sugar atom names, could that be related? I use ff98.
> >Does that make it clearer or do you need further info.
> >I attach the mini2.out file if this can help.
> >Thnks again
> >
> >
> >
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