Re: [AMBER-Developers] Re: Atomic radii assignment for WAT molecules

From: MengJuei Hsieh <mengjueh.uci.edu> Date: Tue, 01 Dec 2009 14:25:46 -0800

----
         else if( GDefaults.iGBparm == 6 ) {
                /* try Alexey's scheme */
                if( sAtomType(aAtomA)[0] == 'N' ||
                sAtomType(aAtomA)[0] == 'n' ) dGBrad = 1.3;
         }
----
So in the case of mbondi2 it is probably okay.
[localhost:~] mjhsieh% cat mbondi.script
set default PBRadii mbondi
saveamberparm TP3 mbondi.prmtop mbondi.inpcrd
quit
[localhost:~] mjhsieh% cat mbondi2.script
set default PBRadii mbondi2
saveamberparm TP3 mbondi2.prmtop mbondi2.inpcrd
quit
[localhost:~] mjhsieh% tleap -f leaprc.ff99SB -f mbondi.script >& /dev/null
[localhost:~] mjhsieh% tleap -f leaprc.ff99SB -f mbondi2.script >& /dev/null
[localhost:~] mjhsieh% sed -n 112p mbondi.prmtop
  1.50000000E+00  8.00000000E-01  8.00000000E-01
[localhost:~] mjhsieh% sed -n 112p mbondi*.prmtop
  1.50000000E+00  8.00000000E-01  8.00000000E-01
Best,
-- 
Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
> From: Carlos Simmerling <carlos.simmerling.GMAIL.COM>
> Reply-To: AMBER Developers Mailing List <amber-developers.ambermd.org>
> Date: Tue, 1 Dec 2009 12:41:23 -0500
> To: AMBER Developers Mailing List <amber-developers.ambermd.org>
> Subject: Re: [AMBER-Developers] Re: Atomic radii assignment for WAT molecules
> 
> sorry- I saw this but was a bit too busy to look into the details. one issue
> is that the OW gets different radii for diff PBradii sets- for example, 0.8
> and 1.2 for mbondi and mbondi2- is this option included? a quick look made
> it seem hardcoded to 0.8
> thanks for doing this!
> carlos
> 
> On Tue, Dec 1, 2009 at 12:20 PM, Scott Brozell
> <sbrozell.rci.rutgers.edu>wrote:
> 
>> Hi,
>> 
>> Carlos please verify that this fixes bug 108 that you reported.
>> 
>> Thanks MengJuei,
>> Scott
>> 
>> On Tue, Dec 01, 2009 at 10:53:44AM -0500, case wrote:
>>> On Mon, Nov 30, 2009, MengJuei Hsieh wrote:
>>>> 
>>>> Forget about PQR, considering the context of algorithms inside the
>> tleap,
>>>> 0.8 Å radii should be the value that LEaP intended to assign.
>>> 
>>> ...applied...thanks...dac
>>> 
>> 
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>> AMBER-Developers.ambermd.org
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