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 - 10:00:03 PDT
