dear amber ,
thank you!
carlos.simmerling .
I will try by using all atoms ,
now i am clear ,
-----------------------
I have another doubt ,
As if now I am doing in vaccum ,
when I solvated the structure in explicit
water , both of them have different number of
water molecules , how to fix both to be the same ,
I read in forum that one can delete the water molecule from
the structure which has more than the needed ,
is there any way of doing it by
taking the close skin of some limit in both so that
one can make same number of molecules .
or is there any other way of doing it
-------------------------------------
thanks in advance !
balaji
UOM
> Date: Sat, 21 Feb 2009 07:35:05 -0500
> Subject: Re: [AMBER] reg.targeted molecular dynamics
> From: carlos.simmerling.gmail.com
> To: amber.ambermd.org
>
> the masks can differ if you want to fit to one group and restrain the
> other. it really depends on the application. for cases like yours you
> probably want both to be the same. have you tried using all atoms in
> the residues in the mask, rather than just some atom names? also, one
> strand may not be "perfect" since the force constant is fairly weak at
> 1. you might try higher.
>
> On Sat, Feb 21, 2009 at 12:10 AM, balaji nagarajan
> <balaji_sethu.hotmail.com> wrote:
> >
> > 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 Mon Feb 23 2009 - 01:08:33 PST
