Dear Users,
I am running TMD in AMBER, at this point i am done with heating and
equilibration steps. I have an open and closed conformation and i want to
span the transition from open to closed.
My Input file for TMD was
TMD: open->closed; target rmsd 1.6; resid 38-134 restrained
&cntrl
imin = 0, ntx = 1, nstlim = 5000, irest = 0,
dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
temp0 = 300.0,
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 = ":38-58,62-85,104-134",
itgtmd = 1, tgtrmsd = 1.6, tgtmdfrc = 1.0,
tgtrmsmask = "(:1-37,59-61,86-103)",
/
&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',
/
and I got an error stating "Targeted molecular dynamics:
tgtrmsd = 1.60000, tgtmdfrc= 1.00000
| INFO: Old style inpcrd file read "
Please suggest where I have gone wrong.
--
Regards,
Pallavi Mohanty
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Received on Wed Dec 31 2014 - 04:00:02 PST
