Hi Carlos,
Thanks for the clarification.
Where are the radii specified then? I don't see them any place else in the prmtop, but maybe I am not looking in the right place.
Best,
Jesper
On Apr 26, 2012, at 9:55 AM, Carlos Simmerling wrote:
> The "radii" in the prmtops are intrinsic Born radii for solvation
> calculations. They are not the vdw radii. Your comments about the vdw radii
> in these force fields are correct. It's just not what that part of the
> prmtop describes.
> On Apr 26, 2012 12:52 PM, "Jesper Sørensen" <jesorensen.ucsd.edu> wrote:
>
>> Hi All,
>>
>> I have a question regarding the radii in my prmtop file. I have built my
>> system in tleap with the input file shown below.
>> I made sure to use tleap -s, so no other input files were pre-loaded.
>>
>> When I look in my prmtop file it says I am using mbondi2 radii. Which I am
>> a bit confused by.
>> Looking through the manuals and the literature, ff10 for proteins is equal
>> to Amber99SB. Amber99 uses as far as I can tell the Amber94 radii - by this
>> I mean I haven't seen any updated vdW parameters in the newer force field
>> papers (ff99, ff99SB).
>> So, should my prmtop file not have the amber94 radii instead of the mbondi
>> radii?
>>
>> I hope you can clarify this for me a bit.
>>
>> Best regards,
>> Jesper
>>
>>
>>
>> %FLAG RADIUS_SET
>> %FORMAT(1a80)
>> modified Bondi radii (mbondi)
>> %FLAG RADII
>> %FORMAT(5E16.8)
>> 1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
>> 1.70000000E+00
>> 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
>> 1.70000000E+00
>> ...
>>
>>
>> #
>> source leaprc.ff10
>> addAtomTypes {
>> { "O3" "O" "sp2" }
>> }
>> loadAmberParams frcmod.tip4pew
>> loadAmberParams frcmod.ionsjc_tip4pew
>> loadAmberParams ../ATP/frcmod.phos
>> loadAmberPrep ../ATP/ATP.prep
>> ATP = atp
>> WAT = T4E
>> set default FlexibleWater on
>> mol = loadPdb pdbfile.pdb
>> solvateBox mol TIP4PEWBOX 10.0
>> addions mol Na+ 18 Cl- 11
>> check mol
>> saveAmberParm mol system.prmtop system.inpcrd
>> quit
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>>
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Received on Thu Apr 26 2012 - 11:30:03 PDT
