Dear Amber users
I am still having problems with the equilibration stage.
My system is a complex of a protein kinase binds to the 6amino-purine.
The whole system contains 247 residues.
First of all, I minimized the solvent (water +ions) keeping the protein's heavy atoms frozen:
&cntrl
imin=1,
maxcyc=1000,
ntb=1,
ntr=1,
cut=10,
restraint_wt = 10.0,
restraintmask=':1-247.CA,C,O,N,H'
/
Afterwards, I wanted to run a short MD keeping frozen the protein's heavy atoms to relax solvent molecules before running a minimization of the whole system:
&cntrl
imin=0,
irest=0,
ntx=1,
ig=-1,
ntb=1,
ntr=1,
cut=10,
ntc=2,
ntf=2,
tempi=300.0,
temp0=300.0,
ntt=3,
gamma_ln=5.0,
nstlim=15000, dt=0.001,
ntpr=100, ntwx=100, ntwr=1000
restraint_wt = 10.0,
restraintmask=':1-247.CA,C,O,N'
Sander immediately stops with the following error message:
vlimit exceeded for step 2; vmax = 144.9409
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 1927 3834 3844
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
If I decrease the dt from 0.001 to 0.0005, sander runs the MD but between each step i got the following messages:
e.g.:
vlimit exceeded for step 4001; vmax = 22.8241
vlimit exceeded for step 4003; vmax = 25.4000
vlimit exceeded for step 4004; vmax = 27.7180
vlimit exceeded for step 4006; vmax = 29.4842
vlimit exceeded for step 4007; vmax = 28.0214
vlimit exceeded for step 4008; vmax = 56.6682
vlimit exceeded for step 4009; vmax = 45.4394
vlimit exceeded for step 4010; vmax = 31.1217
vlimit exceeded for step 4011; vmax = 24.5171
vlimit exceeded for step 4012; vmax = 34.7059
Moreover the TEMP(K) is not around 300.0 at each step but it changes a lot.
All this things suggested me that there is a problem in the structure I am using to run the MD.
After the mininimization stage I checked the TOTAL energy and it was relatively flat at the end of the mninimization. Thus I have no idea how to find out the problem with the minimized structure i am using.
Any suggestions?
I would like the use cheackoverlap in cptraj but is not really clear how it works.
Best,
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 Mon May 12 2014 - 02:00:03 PDT
