AMBER Archive (2009)

Subject: Re: [AMBER] Modification of His

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon May 18 2009 - 07:16:10 CDT

thanks,

I think tihe problem is that I need to find a new pdb name for my nitrogen
atom instead of ND1 which is the same as in histidine. In the leaprc file it
is defined as
    { "N*" "N" "sp2" }

so I cannot use "N*" "YA" "sp2". I have performed a small md simulation of
my residue and the ring is not planar - could that be due to it not being
sp2-hybridized?

On Mon, May 18, 2009 at 1:58 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Mon, May 18, 2009, Jorgen Simonsen wrote:
> >
> > I am trying to modify a HIE residue in my protein which should have
> > different bonding properties with a metal ion.
> >
> > I start xleap by loading the topology and parameter with new modification
> > into xleap but it gives me this error which I thought that should be
> > resolved by the tmp.frcmod file
> > +---Tried to superimpose torsions for: *-CE1-ND1-*
> > +--- With Sp2 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-CG-ND1-*
> > +--- With Sp2 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
>
> First, these are just warnings, and can be ignored (I think.) If you want
> to
> eliminate them, add your new atom type to the addAtomTypes list in your
> leaprc file.
>
> ...good luck...dac
>
>
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