On Thu, Dec 6, 2012 at 10:55 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Greetings,
>
> 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.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Dec 06 2012 - 09:30:02 PST
