Dear Amber Users,
Am trying a simulate a protein+nucleic acid complex. I would like to
restrain distance between atoms of interest at particular distance
geometry for few ns in production run itself (sought of guided
simulation) and then do a free simulation. But am not sure of the
force constant to use for restraining the atoms mentioned in list
rst.dist (in my case). Pls. find below my input files.
I would like to know What is ideal range for 1) restraint_wt and 2)
rk2 and rk3. Request to offer your insights and see if am going right.
Appreciate your time and help.
Thanks
Regards
-Gsmith
#INPUT FILES
Production Run
&cntrl
imin = 0, irest = 1, ntx = 7,
ig=-1, iwrap = 1,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 13.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 5000, ntwx = 10000, ntwr = 10000
nmropt = 1,
restraint_wt = 20.0,
/
&wt type='END' /
DISANG=rst.dist
LISTIN=POUT
LISTOUT=POUT
My rst.dist file looks like this;
#
# 13 CYT 0 42 RNA O2' 3.00 3.20
&rst
ixpk= 0, nxpk= 0, iat= 320, 1348, r1= 2.50, r2= 3.00, r3= 3.20, r4= 3.70,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
&end
#
# 16 ASN ND2 42 DNA O1P
&rst
ixpk= 0, nxpk= 0, iat= 292, 1317, r1= 4.30, r2= 4.80, r3= 4.90, r4= 5.40, &end
#
# 32 ASP OD2 46 DNA O1P
&rst
ixpk= 0, nxpk= 0, iat= 291, 1881, r1= 3.40, r2= 3.90, r3= 4.00, r4= 4.50, &end
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Received on Sat Mar 07 2015 - 03:30:03 PST
