Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 17 Feb 2012 07:49:11 -0500

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
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Received on Fri Feb 17 2012 - 05:00:02 PST
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