AMBER Archive (2007)

Subject: AMBER: bondi radii problems

From: Eddie Men (pckboy_at_gmail.com)
Date: Tue Nov 27 2007 - 21:31:19 CST

Greetings!

I am trying to use igb=7 and I have problems with the prmtop file,
I am trying to use both of these commands:
#set default PBradii mbondi2
set default PBradii bondi

But I dont seem to solve the problem:

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                               
 
 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 134
 Atom 1 has radius 0.000000000000000
  outside of allowed range
 of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with bondi radii.
[qman_at_n

Is there anything wrong with my input?.
Help would be appreciated

Eddie Men

Minimization with Cartesian restraints
&cntrl
imin=1, maxcyc=1000,
ntr=1,
igb=7, ntb=0,
ntf=2, ntc=2,
restraint_wt=10.0,
restraintmask='@PB,PG',
ifqnt=1,
ntwe=10, ntwx=10, ntpr=10,
cut=15,
/
&qmmm
qmmask=':541,542,543',
qmcharge=-4,
qmtheory=1,
qmcut=8,
itrmax=3000,
writepdb=1,
/

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