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.
I have also tried to use parmed.py to change the radii after tleap but
still get the same error. Can someone help me please?
Below is my parameter file:
&cntrl
maxcyc=500, ! 200 steps
imin=1, ! of energy minimization
cut=999.0, ! using an infinite cutoff
igb=8, ! use the optimized GBn model
ntb=0, ! no PBC
ntpr=50, ! intermediate results will be printed every 50 steps
&end
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Dec 06 2012 - 08:00:02 PST
