Dear Amber ,
I have started doing Targeted Molecular Dynamics
for two structurally different system from the same sequence ,
I did it in vaccum after doing all the priliminary steps
and gave a mask to the backbone atoms
my input file is below
-----------------------------------------------------------------
&cntrl
imin = 0,
irest = 0 ,
ntb = 0,
ntxo = 1,
ntx =1,
tempi =300.0
ntb = 0,
ntc=2,
ntr =0,
ntf = 2,
igb = 1,
nscm = 100,
ntwr = 1000
ntpr = 100,
ntwx = 100,
ntwv =100,
ntwe = 100,
ntt = 3,
gamma_ln = 1.0,
temp0 = 300.0
nstlim = 2000000,
dt = 0.001,
cut = 12.0,
itgtmd=1,
tgtrmsd =0.5 ,
tgtmdfrc = 1.0,
tgtfitmask= ":1- 40 . P,O1P,O2P,O5',C5',C4',O4',C1',C4',C6,C5,C2,O2,C4,C3',C2',O3'",
tgtrmsmask= ":1- 40 . P,O1P,O2P,O5',C5',C4',O4',C1',C4,C6,C5,C2,O2,C4,C3',C2',O3'",
/
------------------------------------------------------------------------------------------------------------------------------------
when I gave this to a duplex structure amd the duplex is no more stable it goes in to a structure of a junction ,
which is my reference structure , but one strand is not perfect ,
I have doubt regarding
a) tgtfitmask , here i have selected all the back bone atoms
If one wants to select 1-10 , and 21-30 how it should be given ?
b) Its given in the manual that the tgtfitmask and tgtrmsmask canbe same or different
i am not clear still regarding this
two options ,
so for my first try i gavae all to be same ?
if one wants to give it to be different , what is the basic thing to do ?
thanks in advance
balaji
UOM
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Received on Sun Feb 22 2009 - 01:15:33 PST
