AMBER Archive (2005)

Subject: Re: AMBER: Protein with structural ions

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Apr 12 2005 - 11:09:48 CDT

I don't think you need to use the weight change on REST if it isn't
changing.

look at the output file- does it properly read the restraints? when the
Ca moves,
does the restraint energy change? read the output carefully, it should
tell you what's going on.

Kara Di Giorgio wrote:

> I'm not sure if I formatted everything correctly. It ran, but the
> calcium that I'm trying to restrain is still leaving the protein after
> 8 ps like the restraints weren't there at all. Could someone look at
> my md.in and restraints.f files to see if they can see anything
> majorly incorrect? I'll include them in this message.
>
> Thanks,
>
> Kara Di Giorgio
>
>
> *md.in*
>
> stromelysin and ph1ala MD G4eneralised Born, 12 angstrom cut off Ca
> restraints
> &cntrl
> imin = 0, ntb = 0,
> igb = 1, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 10000, dt = 0.001,
> nmropt = 1,
> cut = 12
> /
> &wt type="REST", istep1=0, istep2=10000, value1=1.0, value2=1.0,
> /
> &wt type='end'
> /
> DISANG = enzph1alarestraints.f
>
>
> *restraints.f*
>
> # distance restraints prepared by hand for Ca
> #( oxygen 1 Calcium upper bound)
> #
> # 79 GLY O 171 CA CA 2.8
> #
> &rst iat= 1278, 2611, r3=2.8, r4= 3.3, ialtd=0, /
> #
> # 76 ASP OD1 171 CA CA 2.8
> #
> &rst iat= 1247, 2611, r3=2.8, r4= 3.3, ialtd=0, /
> #
> # 77 GLY O 171 CA CA 2.8
> #
> &rst iat= 1257, 2611, r3=2.8, r4= 3.3, ialtd=0, /
> #
> # 102 GLU OE2 171 CA CA 2.8
> #
> &rst iat= 1585, 2611, r3=2.8, r4= 3.3, ialtd=0, /

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