[AMBER] ERROR: Regenerate prmtop file with bondi radii

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Thu, 6 Dec 2012 17:55:31 +0200

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
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