Dear Amber ,
thank you !
carlos.simmerling.
TO adjust the buffer size , one has to
keep one of the structure as it is
and have to adjust the other structure
to get equal number of solvent molecule .,
if so the size of the buffer box
can be different .,
I am not clear .,
thanks in advance
balaji
UOM
> Date: Sun, 22 Feb 2009 10:06:32 -0500
> Subject: Re: [AMBER] reg.targeted molecular dynamics
> From: carlos.simmerling.gmail.com
> To: amber.ambermd.org
>
> the easiest way is to adjust the buffer size and run leap again.
>
>
> On Sun, Feb 22, 2009 at 9:45 AM, balaji nagarajan
> <balaji_sethu.hotmail.com> wrote:
> >
> > 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 - 01:14:09 PST
