AMBER: targeted MD

From: Germain Vallverdu <germain.vallverdu.lcp.u-psud.fr>
Date: Tue, 22 Jul 2008 12:08:04 +0200

Hello Amber

I would like to do a targeted MD with amber 9. I found this tutorial which gives an example of mdin file.

http://www.rosswalker.co.uk/tutorials/psc_workshop/Tutorial_six/target_md_dock.html

this is the mdin file

inpcrd->refcrd tgtmd: regular vacuum md, backbone restrained
 &cntrl
        imin = 0, ntx = 1, nstlim = 5000, irest=0,
        dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
        tempi = 100.0, temp0 = 300.0,
        scee = 1.2, cut = 10.0,
        ntpr = 50, ntwx = 50, ntwr = 500,
        ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
        igb = 1, nscm = 0, nmropt = 1, 
        ntr = 1, restraint_wt=0.02, 
        restraintmask=":TAZ | :40-51,73-85,96-113,136-147,207-220.CA",
        itgtmd = 1, tgtrmsd = 5.516, tgtmdfrc = 1.0,
        tgtrmsmask=":TAZ & .S1,C2,C3,N4",
 /
 &wt
        TYPE='TGTRMSD', istep1=1, istep2=1000,
        value1 = 1.000, value2 = 0.0,
 /
  &wt
        TYPE='TGTRMSD', istep1=1000, istep2=0,
        value1 = 0.0, value2 = 0.0,
 /
&wt
   type="END",
 /

It deals with a docking of a complex in a protein. I understood the &cntrl namelist but I do not understand perfectly the &wt namelist. In the &cntrl namelist TGTRMSD is equal at 5.516. Next, in the &wt namelists, TGTRMSD is set at 1.0 from step 1 to step 1000 and finally TGTRMSD is set to 0.0 from 1000 to the end. Is it that ? Finally, is the value of 5.516 used in the simulation ?

I tried to do the tutorial but I had got some difficulties. Is the structure well equilibrated ? If I run the job directly with the files which are on the website, shake crashed and temperature is too high (900K).

Thanks a lot for your help

Germain

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