On Wed, Mar 02, 2011, Baptiste Legrand wrote:
> I have used the typical flow presented in this tutorial:
> http://ambermd.org/doc6/html/AMBER-sh-4.3.html and final production is:
Wow. I didn't realize we still had any Amber6 tutorials sitting around on
line. I'd suggest you look instead at tutorial A4 on the regular tutorial
page, which at least has the virtue of not being more than a decade old.
>
> +---------------------------------------------------------+
> | Production dynamics |
> +---------------------------------------------------------+
> | |
> | Production run |
> | |
> |&cntrl |
> | imin=0, nmropt=1, irest=1, ntx=7, |
> | scee=1.2, cut=9.0, |
> | ntt=1, tempi=300., temp0=300., |
> | ntb=1, tautp=2.0, |
> | ntc=2, tol=0.000001, |
> | ntpr=100, ntwr=999999, ntwx=1000, |
> | nstlim=200000, |
> |&end |
> |&wt type='REST', istep1=0,istep2=1000,value1=1.0, |
> | value2=1.0,&end |
> |&wt type='END'&end |
> |LISTOUT=POUT |
> |DISANG=RST |
> +---------------------------------------------------------+
>
> If I have well understood the NMR restraints are only active during the
> first 1000 steps?
I'm not sure. The &wt namelist given above doesn't seem to make much sense,
since the default value of REST is 1.0 anyway. I guess you should do a run,
and look at the output to see if the restraints go away after step 1000: I
don't think they do, but it's easy enough to find out.
Generally, NMR restraints are kept active for the entire run. The restraints
produced by makeCHIR_RST are designed to not perturb correct states, just to
prevent transitions to bad chirality or bad peptide torsions.
...dac
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Received on Wed Mar 02 2011 - 07:00:03 PST
