AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 09 2009 - 11:28:04 CDT

it might be easiest to add this in the dihedral restraint section in the NMR
restraints. however, this will only work for sander.
another possibility if you are comfortable with the prmtop files is to add
one that leap "likes", and then edit the prmtop to change the atom number in
the 4th position.
there may be better solutions that others know about.

On Tue, Jun 9, 2009 at 12:11 PM, Ben Roberts <roberts_at_qtp.ufl.edu> wrote:

> Hi all,
>
> I'm trying to specify improper dihedrals in a metal cluster using a *.prep
> file. Specifically, I'm wanting to specify impropers between histidine rings
> and nickel ions, which are in different residues.
>
> 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). My immediate reaction would be to try something like "CD2
> CE1 NE1 +M" (or "CD2 CE1 NE1 -M"), but I'm told that +M and -M don't work in
> position 4 and also that +M and -M are reserved for the immediately next and
> immediately previous residue respectively. The nickel does not come
> immediately before all histidines to which it is bound, and while I could
> re-engineer the topology to make that so, it would tend to break the rest of
> the chain.
>
> 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?
>
> Thanks,
> Ben
>
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