Dear Amber User,
I am simulating HCAII using 2CBA.pdb. I am using
CaDA approach. I have changed residue name as given in the paper
"Novel Zinc Protein Molecular Dynamics Simulation: Steps Toward
Antiangiogenesis for Cancer Treatment, Yuan-Ping Pang, J. Mol. Model.
1999,5,196-202," After minimisation I have heated up the system using
following input file,
heating of whole system
&cntrl
imin = 0,
irest = 0,
iwrap = 1,
ntx = 1,
ntb = 1,
ntc = 2,
ntf = 2,
ntt = 3,
ntr = 1,
cut = 20.0,
tempi = 0.0,
temp0 = 300.0,
gamma_ln = 1.0,
nstlim = 25000,
dt = 0.002,
ntpr = 100,
ntwx = 100,
ntwr = 1000
/
Keep protein fixed with weak restraint
3.0
RES 1 265
END
END
But, I am getting a follwing error, and run stopped after a time.
vlimit exceeded for step 3680; vmax = 290.4790
vlimit exceeded for step 3681; vmax = 5167.6693
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 2017 4081 4082
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
So, please give some tips so as I can complete it.
Thanking you
Sanjib
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Received on Wed Jun 20 2012 - 03:30:02 PDT
