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

From: Carlos Simmerling <>
Date: Tue, 04 Jan 2005 07:47:03 -0500

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

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
>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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Received on Tue Jan 04 2005 - 12:53:00 PST
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