correct- perhaps the best is to try it and see how it works.
On Mon, Feb 23, 2009 at 1:45 AM, balaji nagarajan
<balaji_sethu.hotmail.com> wrote:
>
> 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
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > _________________________________________________________________
>> >> > Chose your Life Partner! Join MSN Matrimony FREE
>> >> > http://www.in.msn.com/matrimony_______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _________________________________________________________________
>> > Find a better job. We have plenty. Visit MSN Jobs
>> > http://www.in.msn.com/jobs_______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _________________________________________________________________
> Plug in to the MSN Tech channel for a full update on the latest gizmos that made an impact.
> http://computing.in.msn.com/_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 25 2009 - 01:08:21 PST
