the weight change section is often used to modify variables specified
in the cntrl section. I think that 5.516 is not used by sander. I'm not
sure why it crashes though, maybe Ross or whoever designed the
tutorial can help.
On Tue, Jul 22, 2008 at 6:08 AM, Germain Vallverdu
<germain.vallverdu.lcp.u-psud.fr> wrote:
> 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
>
> --
> Germain Vallverdu
> Laboratoire de Chimie Physique
> Université Paris Sud 11
> germain.vallverdu.lcp.u-psud.fr
> 01 69 15 30 38 / 06 88 59 08 87
> Chacun de nous a son étoile. Suivons la en nous félicitant de la voir chaque
> jour un peu plus loin ! (V. Grignard)
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--
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Received on Wed Jul 23 2008 - 06:07:34 PDT
