Hi Jason,
It makes no sense to me that changing forcefield from ff10 to
leaprc.parmCHI_YIL.bsc could change some C radii. mbondi2 radii was
specified in tleap for GB run. I don't think mbondi2 has 2.2 A radius for C
and this radius value is not allowed to work with igb=7.
NHAI
On Fri, Feb 17, 2012 at 7:49 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Some carbon atom types have a radius of 2.2 Angstroms. Have you looked at
> the code that assigns the atom radii in leap?
>
> You can look at the code that does this in parmed (changeradii.py) if you
> have ready access to the developer files. The logic is exactly the same (it
> was copied out of tleap) and it should be easier to read.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Feb 16, 2012, at 11:38 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > Dear Amber community,
> > I want to generate a topology and coordinate file for an RNA structure
> with
> > parmCHI_YIL.bsc (from Ambertools 1.5, applied bugfix) for GB simulation.
> > Here is the input file for tleap
> >
> > source leaprc.parmCHI_YIL.bsc
> > set default PBradii mbondi2
> > x = loadpdb RNA_ss_UUCG.pdb
> > saveamberparm x RNA_ss_UUCG_1_parmCHI_YIL.bsc.top
> RNA_ss_UUCG_1_B_form.crd
> > savepdb x RNA_ss_UUCG_1_B_form.pdb
> > quit
> >
> > When I got the top file, there are some C atoms having radii of 2.2 A
> > instead of 1.7 A as I used ff10 force field. I used an in-house analysis
> > program to print this information.
> >
> > C8 RG5 2.200
> > C6 RC 2.200
> > C6 RC 2.200
> > C8 RG 2.200
> > C8 RG 2.200
> > C6 RC3 2.200
> >
> > Can you please tell me what happen? Is this because of the bug or I miss
> > something?
> >
> > Best
> >
> > NHAI
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 17 2012 - 08:00:02 PST
