Hi,
I would like to perform Umbrella sampling (US) along RMSD-based coordinates
using targeted MD for a ligand bound to a protein. Bellow my input script:
Umbrella sampling with TMD
&cntrl
ntx=1, irest=0,
ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
cut=12.0,
nstlim=500000, dt=0.001,
nscm=100,
ntb=0, igb=5, gbsa=0,
saltcon=0.1,intdiel=1.0, extdiel=78.5,
cut_inner=12.0,
rgbmax = 12.0,
ntc=2, ntf=2, tol=0.000001,
ntpr=100, ntwr=100, ntwx=100,
itgtmd=1, tgtrmsd = 6.8, tgtmdfrc = 0.1,
tgtrmsmask=“:1-18”,
/
&wt TYPE='TGTRMSD', istep1=1, istep2=1000000,
&wt value1 = 66.8998, value2 = 0.0,
I have three questions:
1) how would I define the window size based on several small RMSD
increments?
2) How do I define cartesian restraints to the non-hydrogen atoms of the
protein while I run the TMD?
3) Can I define only C atoms using tgtrmsmask?
Thanks in advance
--
Tarsis Gesteira
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Received on Fri Dec 30 2016 - 08:00:03 PST
