AMBER Archive (2006)

Subject: Re: AMBER: Ring of dna

From: j j (fantvamp_at_gmail.com)
Date: Fri Jul 14 2006 - 09:25:59 CDT

Maybe in a ring there is no O3T,
try:
desc ade.94
in xleap

2006/7/14, f m <floramactavish_at_hotmail.com>:
>
> I've modified the fileleaprc.ff99 file, and it now adds lots of atoms when
> I
> load it.
>
> I'm now having problems with the bond command. My DNA is made of adenine
> and thymine bases. The format I tried to use to bond the atoms is
>
> bond ade.1.P ade.94.O3T
>
> bond thy.95.P thy.188.O3T
>
> (ie ade for adenine 1 for the base number and P for the atom name)
>
> but this doesn't work. It doesn't recognise this format. I'm not sure
> what
> I'm doing wrong. I'd appreciate any advice.
> Flora
>
> >From: "f m" <floramactavish_at_hotmail.com>
> >Reply-To: amber_at_scripps.edu
> >To: amber_at_scripps.edu
> >Subject: Re: AMBER: Ringof dna
> >Date: Thu, 13 Jul 2006 17:00:48 +0000
> >
> >Thankyou, I'll try that!
> >
> >Flora
> >
> >
> >>From: "David A. Case" <case_at_scripps.edu>
> >>Reply-To: amber_at_scripps.edu
> >>To: amber_at_scripps.edu
> >>Subject: Re: AMBER: Ringof dna
> >>Date: Thu, 13 Jul 2006 09:54:07 -0700
> >>
> >>On Thu, Jul 13, 2006, Flora Mactavish wrote:
> >>
> >> > I am attempting to use amber to analyse a ring of dna.
> >> >
> >> > Is there a command to tell Amber that it is dealing with a ring, or
> any
> >>way
> >> > around this problem?
> >>
> >>You have to modify the leaprc file to do this. Make a copy of whatever
> >>you
> >>are using (probalby leaprc.ff94 or leaprc.ff99) , and look at the
> >>addPdbResMap
> >>section. At the bottom of this section are commands that make the
> default
> >>first residue a "5" and the default final residue a "3"-type
> residue. You
> >>don't want that for a circle -- you could actually remove the entire
> >>addPdbResMap section for your copy, and load that instead of the default
> >>one.
> >>
> >>Don't forget to use the "bond" command to add the bond between the first
> >>and
> >>last residues of the circle.
> >>
> >>...good luck...dac
> >>
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