AMBER Archive (2004)

Subject: AMBER: Deeper problem with the energetics of the system

From: nlxc (nlxc2000_at_yahoo.com)
Date: Fri Jun 18 2004 - 12:56:52 CDT

Hi,
 
I am running MD for a system of protein-ligand complex based on the following procedures.
 
1) use solvatebox to add 3 A TIP3P WATBOX around complex(~18000 atoms total)
2) neutralize the system by turnning off the charges of three residues which are most far away from ligand.
3)run 5000 rounds of minimization with protein+ligand restrained. (only water allowed to move)
----------------------
min setting
&cntrl

  ntpr = 10, ntwx = 0, ntwr = 10,

  ntf = 2, ntb = 1,
  cut = 8.5, nsnb = 999999,

  ibelly = 0, ntr = 1,

  imin = 1,
  maxcyc = 5000,
  ncyc = 4000,
  dx0 = 0.1, dxm = 0.1, drms = 0.0001,

  ntc = 2, tol = 0.0005,

 &end
Hold the protein & ligand restrained
500.0
RES 1 266
END
END
----------------------
4)run MD with allowing only residues and water within 20A of ligand to move under the condition of ntb=2.
 
&cntrl
   imin = 0, nmropt = 1, ntx = 1, irest = 0,
   ntwx = 500, ntpr = 100, ntwr = 100, iwrap = 0,
   ntf = 2, ntb = 2,
   cut = 8.5, nsnb = 25,
   ibelly = 0, ntr = 1,
   nstlim = 100000, t = 0.0, dt = 0.002,
   temp0 = 298.0, tempi = 0,
   ntt = 1, tautp = 1,
   ntc = 2, tol = 0.00001,
   ntp = 1, taup = 1,
 &end
 &wt
   type='TEMP0', istep1=0, istep2=25000,
                 value1=0.0, value2=298.0,
 &end
 &wt
   type='TEMP0', istep1=25000, istep2=100000,
                 value1=298.0, value2=298.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end
-- restrain
5000.0
RES 2 2
RES 78 78
RES 105 106
RES 109 109
RES 124 124
........
RES 1026 1026
RES 1056 1057
RES 1059 1059

------------------------------------------------------------------------------
 
But I always got the following error after even the first round of MD
 
vlimit exceeded for step 2; vmax = 36.0015791
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 2139 4275 4276
Note: This is usually a symptom of some deeper
problem with the energetics of the system.

-------------------------------------------------------------------------------
 
If I removed the restrain to allow all atoms to move, the MD is able to run without any problem. But I can't afford to run MD for the whole protein.
 
Could anybody please let me know how to fix this problem and allow only part of system to move in MD? Thanks in advance. Your help will be highly appreciated!
 
Nan
 

 

                
---------------------------------
Do you Yahoo!?
Yahoo! Mail Address AutoComplete - You start. We finish.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu