Dear community,
I am trying to do a steered MD of a protein of 56
residue long. The initial distance between CA atom of 1st residue (atom no
2) and CA atom of 56th residue (atom no 905) is 29A. My input and dist.RST
files are as follows
pro.in>
Sample pulling input
&cntrl
nstlim=5000000, cut=99.0, igb=1, saltcon=0.1,
ntpr=500, ntwr=500, ntt=1,
ntx=1, ntwx=500, ig=256251,
ntc=2, ntf=2, tol=0.000001,
dt=0.002, ntb=0, tempi=300., temp0=300.,
jar=1
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LIST=POUT
dist.RST>
# Change
&rst iat=905,2, r2=29.5, rk2=5000., r2a=50.0, /
The output is file is giving errors
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 343.74 PRESS =
0.0
Etot = 3687.1261 EKtot = 778.3610 EPtot =
2908.7651
BOND = 12.4186 ANGLE = 207.4832 DIHED =
678.5772
1-4 NB = 802.1944 1-4 EEL = 3296.4852 VDWAALS =
14.2383
EELEC = -3938.2112 EGB = -1498.9728 RESTRAINT =
3334.5521
EAMBER (non-restraint) = -425.7870
------------------------------------------------------------------------------
NMR restraints: Bond = 3334.552 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 0; vmax = 302.9507
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 7 1 2
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I dont know what to do. Please help. By the way is there any tutorial for
steered MD for Amber 9.
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Received on Tue Mar 23 2010 - 06:00:02 PDT
