Thanks you very much - I have been looking at chapter 6 for quite a while
and earlier post but I am still quite puzzled how to make an angle
restraint between three atoms?
There are some very nice examples on distance and torsion/dihedral angles
but I have not been able to find one for an angle between three atoms
(A-B-C) - where would I find that?
I could find this example for sander - "angle (:21.C5' :21.C4' 108)" but
again not for pmemd also this example only two atoms are defined.
Any help appreciated. Thanks
On Fri, Feb 14, 2014 at 12:45 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Feb 14, 2014, Jorgen Simonsen wrote:
> >
> > I am trying to make restraints to zinc ions in a protein I would like to
> > run a MD simulatoin on but I get the following error :
> >
> > # makeDIST_RST
> > Currently configured for up to 50000 atoms
> > Using MAP file ~/amber12/dat/map.DG-AMBER
> > ERROR no map function for ZN ZN :data= 333 ZN ZN 23 HID
> > NE2 2.1
> >
> > I ran the cmd
> >
> > ~amber12/bin/makeDIST_RST -upb rst_file -pdb tmp.pdb -rst RST.dist
> >
> > the 7-column file looks like this
> >
> > 333 ZN ZN 23 HID NE2 2.1
> >
>
> The default in makeDIST_RST is to not map an atom to itself; the original
> intent was for NMR data, to be very conservative and treat unknown
> atom/residue entries as an error. That can be an effective filter against
> typos in input restraint files (which might be rather large files).
>
> So, you just have to edit ~/amber12/dat/map.DG-AMBER, and add a ZN residue
> entry, and have it map ZN to ZN. Once you look at the file, the format
> will
> be obvious.
>
> (We probably should add some command-line option to map atoms to
> themselves if
> they are not otherwise mapped. It's actually on my to-do list, or perhaps
> more
> realistically, my "to-not-do" list....)
>
> ...dac
>
>
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Received on Fri Feb 14 2014 - 14:30:02 PST
