AMBER Archive (2007)

Subject: Re: AMBER: EXTRA_PTS: frtype 2 Should not be here

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 16 2007 - 11:33:52 CDT

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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