AMBER Archive (2009)

Subject: Re: [AMBER] reg.targeted molecular dynamics

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Feb 22 2009 - 09:06:32 CST

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_at_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_at_gmail.com
>> To: amber_at_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_at_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_at_ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_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_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber