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.uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183
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Received on Fri Feb 20 2009 - 01:07:41 PST
