Le 26/02/2011 22:47, case a écrit :
> On Fri, Feb 25, 2011, Baptiste Legrand wrote:
>> After running antechamber, I create random structures of an organic
>> compound with an initial heating stage at 1000K for example (to solve
>> NMR structures). Nevertheless during this stage and a short minimization
>> few peptide bonds became cis instead of the usual trans configuration.
>> What is the best way to fix this? to add dihedral restraints?
> yes...adding dihedral restraints is appropriate here. The script makeCHIR_RST
> will do this for you (see Section 6.7.3 of the Users' Manual). It also adds
> constraints to prevent chirality flips during high-temperature annealing,
> which is usually what you want. Check the output file before using,
> especially if you have any peptide bonds that *should* be cis.
>
> ...good luck....dac
>
>
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Thanks for your answer david. I have few questions about to the solvent
refinement. I have used the typical flow presented in this tutorial:
http://ambermd.org/doc6/html/AMBER-sh-4.3.html and final production is:
+---------------------------------------------------------+
| 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? Is it more "correct" during the production run to
inactive or active the NMR restraints?
In this case, the RMSD between my set of structures sensitively increase
comparing to those after the SA. That may be explain by the run at 300K
and the absence of NMR restraints.
thanks,
Baptiste
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Received on Wed Mar 02 2011 - 02:30:02 PST
