AMBER Archive (2009)

Subject: RE: [AMBER] reg.Targeted molecular dynamics

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Feb 18 2009 - 08:07:09 CST

dear amber ,
thank you ! for your reply
simon becker,

the problen is i have choosen
DNA structures both of then are entirely different structures
but have same atoms ,
is it reasonableto try out them first in vaccum
and , i have a another doubt if one do it in explicit solvent ,
for both the molecule should have the same number of water molecules ,

tahnks in advance !
balaji
UOM

 
> Date: Wed, 18 Feb 2009 12:38:54 +0100
> From: simon.becker_at_uni-konstanz.de
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] reg.Targeted molecular dynamics
>
> hi balaji,
>
> you know that the protein moves and rotates around in your simulationbox
> during simulation. subsequently the rms between target and reference
> fluctuates with simulation time. therefore you superimpose both
> structures acording to the atoms specified in tgtfitmask to get reliable
> rms-values. the tgtrmsmask specifies the atoms you want to apply force
> to. e.g. if you want to see a ligand move in a protein you get the
> protein as fitmask and the ligand as rmsmask. The force applied to the
> ligand is calculated using the falues specified in tgtrmsd and tgtmdfrc
> (refer to your amber manual for the correct fromula).
>
> hth
> simon
>
> balaji nagarajan schrieb:
> > dear amber ,
> >
> > I am doing TMD using amber ,
> > I have took two structures
> > and minimized them and equillibriated them
> > separately and with that ,
> > I have fixed one as the reference structure and the other as a Target ,
> > I have started doing TMD in vaccum .
> > The two structures are having same number of atoms ,
> > and they have a rmsd difference greaterthan 10 .
> > as if now I am making the input file ,
> > my input file is as follows
> >
> > &cntrl
> > imin = 0,
> > irest = 0 ,
> > ntb = 0,
> > ntxo = 1,
> > ntx =1,
> > tempi =300.0
> > ntb = 0,
> > ntc=2,
> > 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 = 10000000,
> > dt = 0.001,
> > cut = 12.0,
> > itgtmd=1,
> > tgtrmsd =15 ,
> > tgtmdfrc = 1.0
> > tgtfitmask= ":",
> > tgtrmsmask=":"
> >
> > /
> >
> > i didnot gave any mask , and i want to know wether i have given the TMD flags correct ,
> > the two flags are confusing ,
> > tgtrmsd
> > tgtmdfrc
> > in the way how we have to give values for it while doing the simulation based on the two structures of interest ,
> >
> > and how one can give the force to the target molecule ,
> >
> > thanks in advance !
> > balaji
> > UOM
> >
> >
> >
> >
> >
> >
> > _________________________________________________________________
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> >
>
>
> --
> Simon Becker
> Dept. of Biology
> Molecular Bioinformatics
> Box M647
> Universitaet Konstanz
> D-78457 Konstanz
>
> mail: simon.becker_at_uni-konstanz.de
> Tel: 0049 7531 882900, Fax: 3183
>
>
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