Dear Dr David,
Thank you very much for your reply, I will try in this way.
Dr. Dilip H. Dagade
On 8/16/07, David A. Case <case.scripps.edu> wrote:
>
> On Thu, Aug 16, 2007, Dilip Dagade wrote:
>
> > I loaded the leap using the following command in terminal window:
> >
> > $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc .ff02EP
> >
> > In xleap, I given following commands to prepare the topology and
> coordinate
> > files:
> >
> > model=loadpdb 4INSm.pdb
> > addions model Na+ 0
> > solvateoct model TIP3PBOX 8
> > saveamberparmpol model model_wat.prmtop model.wat.prmcrd
> >
> > The pdb file that I loaded in xleap is attached here.
> >
>
> Your pdb file has CYX residues, but you did not use "bond" commands to
> create the disulfide bonds. This leaves dangling bonds at the CYX
> position,
> which confuses the extra points code. Remember that (unless you have
> CONECT
> records in your pdb file) LEaP will not automatically create disulfide
> bonds:
> you have to do it manually. [Wei: does sleap fix this problem?]
>
> That said, you should be very careful with the ff02EP force field. At a
> minimum, you should download the Amber 9 force field files from the Amber
> web
> page (or upgrade to Amber 9), to get the "r1" revisions to the parameters
> (see
> J. Comput. Chem. 27: 781, 2006). But my (non-exhaustive!) tests show that
> problems crop up when you combine polarizability with extra points. Yong
> Duan
> (or people in his group) may want to chime in here, but my personal view
> is
> that ff02polEP.r1 is not really ready for routine use. [ff02pol.r1,
> without
> the extra points, seems fine.] You may still want to explore this, but
> should
> be aware of potential problems.
>
> ...good luck...dac
>
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--
Dr. Dilip H Dagade,
Department of Chemistry,
Shivaji University,
Kolhapur - 416 004 (India)
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Received on Sun Aug 19 2007 - 06:07:27 PDT
