Hi,
I am trying to do a NPT simulation with a protein structure restraining
Restrain 2 to 20 residues
1.0
Restrain the CA atom of first residue strongly
1.0
Before this particular run i carried out a minimization amd Simulated
annealing step with restrains.
50.0
RES 2 20
Restrain the CA atom of first residue strongly
1000.0
I wish my system should be at constant pressure 200.0 .
*******************************************************************************
Error:
vlimit exceeded for step 6; vmax = 59.1247
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 78 140 141
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
*******************************************************************************
I have tried to search in google and read the messages posted previously
by others, and reduced the restraints as per their suggestions. Yet, i could
not able to run my system
$ Can someone please advice me here. below is my input file
Input file is
--------------------------------------------------------------------------------------------------------------------
&cntrl
imin = 0, ntx = 7, irest = 1,
ntpr = 100, ntwx = 500, ntwe = 0, ntwprt=0,
ntc = 2, ntf = 2,
nstlim = 50000, dt =0.002,
tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
ntb = 2, ntp = 1,taup=0.2, pres0=200.0,
ntr=1,iwrap=1,cut=10.0
&end
Restrain the heavy atoms
1.0
RES 2 20
END
Restrain the CA atom of first residue strongly
1.0
FIND
* CA * *
SEARCH
RES 1
END
END
Amber Version : 9
Operating System : Linux
--------------------------------------------------------------------------------------------------------------
Thanks in advance,
-Vikram
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Received on Wed Jan 03 2007 - 06:07:26 PST
