AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Feb 21 2009 - 06:35:05 CST

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
>
>
>
>
>
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