Dear Amber users
I want to run a MD (heating fro 0 to 300K) with restraints on the solute (solute = protein-ligand complex).
First of all, I minimized the system in 2 steps.
1) only solute restrained
2) all atoms free
The input file for the 2nd step is:
&cntrl
imin=1,
maxcyc=10000,
ncyc=2500,
ntb=1,
igb=0,
cut=12
/
Then I used the minimized structure as input for the MD heating stage.
The MD was immediately stopped with the following error:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -113244.2583 EKtot = 0.0000 EPtot = -113244.2583
BOND = 140.4824 ANGLE = 683.5019 DIHED = 2272.1178
1-4 NB = 785.8019 1-4 EEL = 8760.7170 VDWAALS = 17150.2089
EELEC = -143037.0883 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.1423E-03
------------------------------------------------------------------------------
vlimit exceeded for step 1; vmax = 50.5448
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 1924 3839 3846
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I think the error is related to the minimized structure I am using as input.
Is there a way to check if the minimization went well (e.g.: an easy way to plot the total energy vs time steps)?
How to check if it necessary minimize for a longer or shorter time?
The last step of the minimization is the following:
NSTEP ENERGY RMS GMAX NAME NUMBER
10000 -1.0588E+05 6.6968E-01 7.0286E+01 N9 3834
BOND = 7509.5321 ANGLE = 683.5019 DIHED = 2272.1178
VDWAALS = 17150.2089 EEL = -143037.0880 HBOND = 0.0000
1-4 VDW = 785.8019 1-4 EEL = 8760.7170 RESTRAINT = 0.0000
While the enrgy at the step 0 of the MD is:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -113244.2583 EKtot = 0.0000 EPtot = -113244.2583
Could the difference in the energy values had influenced the error I got? If yes, I can solve it?
Thank you
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
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Received on Thu May 08 2014 - 09:30:03 PDT
