I want to calculate the mm/pbsa between a ligand and a protein. When I run:
$AMBERHOME/exe/sander -O -i density.in -o density.out -p
ras-raf_solvated.prmtop -c heat.rst \
-r density.rst -x density.mdcrd -ref heat.rst
The error happened:
---------------------------------------------------
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 = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 11197800
| TOTAL SIZE OF NONBOND LIST = 11197800
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -170815.7622 EKtot = 0.0000 EPtot =
-170815.7622
BOND = 154.6188 ANGLE = 608.1955 DIHED =
2270.4872
1-4 NB = 913.2979 1-4 EEL = 11917.0978 VDWAALS =
48825.5422
EELEC = -330729.7487 EHBOND = 0.0000 RESTRAINT =
95224.7472
EAMBER (non-restraint) = -266040.5093
Ewald error estimate: 0.1646E-03
------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 251.84 PRESS =
0.0
Etot = -136672.3541 EKtot = 31241.4860 EPtot =
-167913.8401
BOND = 2037.0652 ANGLE = 5657.9467 DIHED =
3621.1226
1-4 NB = 1494.2678 1-4 EEL = 11687.0045 VDWAALS =
37542.1375
EELEC = -271841.5123 EHBOND = 0.0000 RESTRAINT =
41888.1280
EAMBER (non-restraint) = -209801.9681
Ewald error estimate: 0.1549E-03
------------------------------------------------------------------------------
vlimit exceeded for step 168; vmax = 49.4150
vlimit exceeded for step 171; vmax = 99.2573
vlimit exceeded for step 173; vmax = 33.3404
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 2150 4380 4440
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Here is my density.in file:
heat ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=1.0,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntr=1, restraintmask=':1-242',
restraint_wt=2.0,
/
what about it? how should I do?
Thank you!
GuanXin
2009.04.02
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 03 2009 - 01:13:16 PDT
