AMBER Archive (2009)

Subject: [AMBER] Help: An error happened when I calculate mm/pbsa

From: thirsty (thirstymail_at_gmail.com)
Date: Thu Apr 02 2009 - 03:12:25 CDT

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
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