AMBER Archive (2009)

Subject: Re: [AMBER] Improper dihedrals between residues?

From: Ben Roberts (roberts_at_qtp.ufl.edu)
Date: Tue Jun 09 2009 - 14:12:07 CDT

Hmm. So, if I understand you, you're saying that the improper specs in
parm files are essentially ignored anyway?

If that's so, I'll just use rdparm to see what's going on. And if I
need to add an improper, it seems safest to follow Carlos' suggestion
and use an NMR-type restraint.

Thanks for the clarification!

Ben

On 9/6/2009, at 3:04 p.m., Bill Ross wrote:

>> If I try to do so in the IMPROPER section of a given residue's entry
>> in the *.prep file, leap complains about the nickel ion not existing
>> in the residue (unsurprisingly). ...
>> So, my question is: is it possible to manually specify an improper
>> dihedral which crosses residue boundaries like this, and if so, how
>> might I go about doing so?
>
> The IMPROPER section in prep.in files has only one purpose: these
> 'impropers' are remembered by leap and regurgitated on saveamberparm
> for comparison with the true impropers that leap derives by matching
> atom types in the appropriate topology to the impropers in parm.dat
> and frcmod files.
>
> A long time ago, impropers were defined in the prep file and the
> programs prep, link, edit and parm built everything with them.
> Once leap was introduced, the method of matching impropers changed
> to match that for bonds, angles and dihedrals (the only diff is
> that leap allows there to be no improper). I added the printing
> of prep.in impropers to aid in debugging leap and for people tuning
> the improper parameters.
>
> If you want to have an old-style improper span a residue, you will
> have to program it in leap. Probably it is easier to user rdparm to
> check which impropers from parm.dat/frcmod files are getting applied
> than to worry about the legacy handling in leap.
>
> Bill
>

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