AMBER Archive (2009)

Subject: [AMBER] Fix Residue continued...

From: Vishal Maingi (maingipaws_at_yahoo.co.in)
Date: Thu Jun 18 2009 - 13:48:03 CDT

> >
> > Dear amber users,
> >
> > I am new to amber and
> > this is in continuation with query on Fix.... by
> Yunjei Zhao
> >
> >
> > as already written the input file "ambermask" I have
> seen it
> >
> > can we not fix residue by using Group or atom in 
> input file after / as
> > given in DNA amber tutorial by knowing which residue
> is which?
> >
> > I am using polymer. I solvated with water and
> hence polymer become
> > solute. now in order to know my file I used "desc"
> command. by this I get
> > number of residues with my polymer being shown as
> number res 1 (polymer now
> > residue) and rest of being shown as wat residues.
> >
> > input file
> > &cntrl
> >
> >  *
> > *
> > *
> >  *
> >  /
> > title
> > value
> > RES number(to be fixed)
> > END
> > END
> >
> >  my question is, can we not fix the residue
> by above type of input file
> > as shown if we know the residue number in our
> structure. I am not able to
> > understand and sure about this

any suggestion will be appreciated
> >
> > thanks
> >
> > Vishal
> > India
 

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