NHAI,
It it likely that leap is not recognizing the atom types
used in parmCHI_YIL. You might need to do some
hacking around to get it correct.
As an additional note, some of the PB code does not
recognize some of the newer atom types (like chiOL),
at least in amber11. I haven't checked the developer
code.
--Niel
________________________________________
From: Mike NG [nhai.qn.gmail.com]
Sent: Friday, February 17, 2012 8:47 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA
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
>
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Received on Fri Feb 17 2012 - 08:30:02 PST
