> > I am trying to use the optimized GBn model (igb=8). Below is the sequence
> > of commands I issue in tleap:
> >
> > tleap -s -f /home/thomas/Programs/amber12/dat/leap/cmd/leaprc.ff99SBildn
> > loadAmberParams frcmod.ff99SBnmr
> > set default pbradii mbondi3
> > mol = loadpdb x15y120z15.pH6.pqr
> > saveAmberParm mol structure.prmtop structure.inpcrd
> > quit
> >
> > But when I run energy minimization I get the following error:
> >
> > Atom 521 has radius 2.20000000000000 outside of
> allowed
> > rang
> > e
> > of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with bondi
> > radii.
> >
>
> What is atom 521? My guess is that it is the CG2 atom of an isoleucine.
> Previous convention assigned C# atom types (where # is an integer) to
> nucleic acids, and that assumption appears to have been built into the
> radii determination for the mbondi3 radius set. Specifically, it sets all
> C3 atom types to radius 2.2, and all other C atom types to 1.7 (which is
> within the desired range).
>
> You can see the radii logic in
> $AMBERHOME/AmberTools/src/parmed/ParmedTools/changeradii.py. It's
> significantly more convoluted in the tleap source code.
>
> You can fix this in ParmEd with the following commands:
>
> changeRadii mbondi3
> change RADII :ILE.CG2 1.7
>
> This will 1) change the radius set to mbondi3, and 2) change all RADII in
> the mask :ILE.CG2 to 1.7 (which is the 'intended' radius selection for
> mbondi3).
>
> Or, of course, you can use ff12SB or another 'official' Amber force field
> instead if ff99SBildn.
>
> HTH,
> Jason
>
> P.S. ParmEd and tleap should give identical radii for the same keyword,
> barring of course instances when individual radii were changed by ParmEd.
>
>
Hi Jason.
I guess the indices in AMBER start from 1. I don't want to confuse it with
VMD where the indexing starts from 0. If the previous is true then atom 521
is the CG2 carbon of an ILE. Otherwise it is the HG21 hydrogen of an ILE.
What radius should that hydrogen have? 1.2 A.?
thanks,
Thomas
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Received on Thu Dec 06 2012 - 14:00:02 PST
