AMBER Archive (2002)

Subject: Re: restraining atoms

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Oct 17 2002 - 12:54:37 CDT

Hi,

I did realize my mistake yesterday in the end, I put the wrong names in
the wrong columns, indeed the first column should be the names and the
second the force field types. Sorry for the mistake and thanks for the
reply.

Ioana

On Thu, 17 Oct 2002, Lepsa wrote:

> Dear Ioana,
> are you sure CD? are atom TYPES? I suppose these are names. TYPES should be
> two character long...... Yours are maybe NAMES ( i.e. the 1st column?)
>
> Hope this helps,
>
> Martin Lepsik
>
>
> > Hi,
> >
> > I am trying to restrain some of the heavy atoms in the structure
> >
> > ****************************
> > Restrain the 7AHL heavy atoms I
> > 5000.0
> > FIND
> > * CA * *
> > * CB * *
> > * CD * *
> > * CD1 * *
> > * CD2 * *
> > * CE * *
> > * CE1 * *
> > * CE2 * *
> > * CE3 * *
> > SEARCH
> > RES 1 2051
> > END
> > **********************
> >
> > but I see in the output file that sander is not able to recognize the
> > three character definition of the atoms (CD1, CD2, CE1, CE2, CE3)
> >
> > **************************************
> > GROUP 1 HAS HARMONIC CONSTRAINTS 5000.00000
> > ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED
> > IN GROUP BELOW
> >
> > GRAPH NAME = * SYMBOL = CA TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CB TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CD TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CD TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CD TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
> > GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
> > GRP 2 RES 1 TO 2051
> > Number of atoms in this group = 1260
> > ****************************************
> >
> > What is the correct way to define these atoms so that sander recognizes
> > them (the names are assigned in Leap).
> >
> > Thank you,
> > Ioana
>
>