Dear amber users,
I am a new subscriber for amber. I am trying to do an umbrella sampling
for a 12 base pairs two DNAs separated by certain distance using amber8.
The reaction coordinate is along the two center of mass of DNA. The
distance restraint file I used is according to amber8 manual (pg 173) and
is as follows:
&rst
iat= -1,-1, nstep1=1, nstep2=6000,
iresid=1,irstyp=0,ifvari=1,ninc=0,imulti=0,ir6=0,ifntyp=0,
r1=0.00000E+00, r2=112.0000, r3=112.0000, r4=99.0000,
rk2=5.0000, rk3=5.0000,
r1a=0.00000E+00, r2a=110.0000, r3=110.0000, r4=99.0000,
rk2a=5.0000, rk3a=5.0000,
igr1 = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 0,
grnam1(1) ='P', grnam1(2)= 'P', grnam1(3)='P', grnam1(4)='P',
grnam1(5)='P', grnam1(6)='P', grnam1(7)='P', grnam1(8)='P',
grnam1(9)='P', grnam1(10)='P', grnam1(11)='P', grnam1(12)='P',
grnam1(13)='P', grnam1(14)='P', grnam1(15)='P', grnam1(16)='P',
grnam1(17)='P', grnam1(18)='P', grnam1(19)='P', grnam1(20)='P',
grnam1(21)='P', grnam1(22)='P', grnam1(23)='P', grnam1(24)='P',
igr2 =
25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,0,
grnam2(1) ='P', grnam2(2)= 'P', grnam2(3)='P', grnam2(4)='P',
grnam2(5)='P', grnam2(6)='P', grnam2(7)='P', grnam2(8)='P',
grnam2(9)='P', grnam2(10)='P', grnam2(11)='P', grnam2(12)='P',
grnam2(13)='P', grnam2(14)='P', grnam2(15)='P', grnam2(16)='P',
grnam2(17)='P', grnam2(18)='P', grnam2(19)='P', grnam2(20)='P',
grnam2(21)='P', grnam2(22)='P', grnam2(23)='P', grnam2(24)='P',
/
my sander input file is :
&cntrl
nmropt = 1,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
ntwprt = 0, ntwr = 500,
ntf = 2, ntb = 1, dielc = 1.0,
cut = 9.0, nsnb = 10,
scnb = 2.0, scee = 1.2,
ipol = 0,
ibelly = 0,
imin = 0,
nstlim = 100000,
nscm = 1000,
t = 0.0, dt = 0.001,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
ntt = 1,
tautp = 1.0,
vlimit = 20.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.5,
ntc = 2, tol = 0.0005,
/
&ewald
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG= distcom112.RST
DUMPAVE=umbcom.112
The output file and trajectory files didn't have any errors written, but
the umbcom.112 file that has been generated during the run should have
restraint value of distance which was not printed, instead it is like this
Restraints on step 0:
0.000
Restraints on step 10:
0.000
Even with varying the force constant (rk2, rk3 ) values of 5-25kcal/mol
also it didn't print any value.
Can any one tell me where is the mistake? Is that i cant define the
residue in the center of mass restraint? If so how should be the input
distance restraint file for umbrella sampling?
Thanks in Advance
usha
Inorganic and physical chemistry
Indian Institute of Science
Bangalore -12
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Received on Sun Jun 03 2007 - 06:07:27 PDT
