AMBER Archive (2002)

Subject: minimization probs

From: Amesh Patel (paxabp_at_nottingham.ac.uk)
Date: Tue Jun 11 2002 - 10:57:12 CDT

hiya!!
i have a system consisting of a protein with a carbohydrate ligand. when
i try to minimize it using the following input file, the end structure
isn't actually a minimium energy strucutre. so when i try to minimize it
further by another 500K steps, the energy and rms do indeed decrease but
then halfway through they increase and don't stop increasing (not quite
the point of minimization methinks). i have set the cut to 999ang and
the nsnb to 99999999 but the electrostatic energy figure goes off the
scale and the thing never minimizes. i have tried to do MD at 10 kelvins
using the initial minimized structure but the temperature went to 6000+
kelvins and i assumed it had blown up by then anyway. i eventually want
to do belly dynamics concentrating on the actual binding site of my
ligand but i am not able to do this until the energy has been sorted out
at the minimization stage (believe me, i have tried to ignore and plod
on but it just won't let me!). do any of you have any welcome words of
wisdom concerning the above probs??? please help, i may lose my mind
very soon. thanx+bybye. amesh patel

here is the first minimztn input file (amber7):

 &cntrl
   imin=1,
   maxcyc=100000,
   ntpr=200,
   cut=8,
   nsnb=999999,
   ntmin=2,
   scee=1.2,
   ntb=0,
 &end