Hello,
I've never actually used makeDIST_RST before, but the usage message suggests
that it's a utility for converting DIANA restraints to amber format. Look
at the suggested part of the manual I sent earlier (Chapter 6 in amber11).
You should set nmropt=1 in the &cntrl namelist, then create a distance
restraint file.
There should be an example in the test directory $AMBERHOME/test/umbrella.
This has set up an umbrella potential around a torsion. Along with the
description, it should help you create a distance restraint for your
application.
Good luck!
Jason
On Mon, Dec 6, 2010 at 6:41 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> I got a error after running
> makeDIST_RST -upb 7col.dist -pdb 2hbs.pdb -rst RST.dist
> ------------------------------------------------------------
> ERROR no map function for CA ARG :data= 1365 ARG CA 654 GRA C 60.0
>
> in the 7col.dist file, I have
> ---------------------------------------
> 1365 ARG CA 654 GRA C 60.0
> -----------------------------
>
> So I changed CA to CD according to map.DG-AMBER file and I have agiain,
> ----------------------------------------------------------------
> ERROR no map function for C GRA :data= 1365 ARG CD 654 GRA C 60.0
> -----------------------------------------------------------------
>
> How do I have map function for carbon from GRA residue made by antechamber?
> Bongkeun Kim
>
>
> Quoting Bongkeun Kim <bkim.chem.ucsb.edu>:
>
> > Hello Jason,
> >
> > I started with the simple thing first.
> > I just picked up one carbon atom on surface (reg name=GRA, reg # 1153).
> > And chose C aplha from the center residue(#22) of my peptide.
> > And run makeDIST_RST
> >
> > makeDIST_RST -upb 7col.dist -pdb 2hbs.pdb -rst RST.dist
> >
> > in the 7col.dist file, I have
> > ---------------------------------------
> > 22 ARG CA 1153 GRA C 50.0
> > -----------------------------
> > with the max distance <50A
> >
> > Do you think this is a correct way to set up the distance restraint?
> > Thank you.
> > Bongkeun Kim
> >
> >
> > Quoting Jason Swails <jason.swails.gmail.com>:
> >
> >> You can use the nmropt functionality. See the description in Chapter 6
> in
> >> the amber11 manual (the functionality is the same in amber10 as well).
> >>
> >> Good luck!
> >> Jason
> >>
> >> On Mon, Dec 6, 2010 at 4:40 PM, Bongkeun Kim <bkim.chem.ucsb.edu>
> wrote:
> >>
> >>> Hello,
> >>>
> >>> I'm going to use the implicit solvent MD study of peptide on surface.
> >>> Because of absence of the periodic boundary condition, I want to give
> >>> a distance restraint between flat surface molecule and the peptide
> >>> whose maximum distance between the centers of mass will be less than
> >>> 20Angstrom.
> >>> Do you have any idea how to set this up?
> >>> Thank you.
> >>> Bongkeun Kim
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Dec 06 2010 - 17:00:04 PST
