Dear Amber users,
My complex contains DNA and protein. I would like to use ibelly to keep
frozen the complex and allowed water to move. My input file contains:
energy minimization for DNA and protein
&cntrl
imin = 1,
maxcyc = 2000,
ncyc = 500,
cut = 12,
ntb = 1,
ibelly = 1,
/
RES WAT
END
END
after short run, calculations stopped:
the out file contains>
Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!
LOADING THE BELLY ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
RES WAT
Number of atoms in this group = 0
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.00000017
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 0
| TOTAL SIZE OF NONBOND LIST = 0
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.0972E+06 NaN 0.0000E+00 N 1
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = -624.5497 EEL = -1096564.5563 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
what is wrong?
best regards
Urszula
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
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Received on Tue Mar 25 2014 - 06:30:02 PDT
