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.The Basic difference between both
the structure is the first helix that moves out and has an RMSD of 24.7 for
1-37 residues
My Input file for TMD was
TMD: open->closed; target rmsd 1.6; resid 38-134 restrained TMD:
open->closed; target rmsd 1.6; resid 38-134 restrained
&cntrl
imin = 0, ntx = 5, nstlim = 5000, irest = 1,
dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
temp0 = 300.0,
cut = 16.0,
ntpr = 1, 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 = ":38-134",
itgtmd = 1, tgtrmsd = 24.7, tgtmdfrc = 1.0,
tgtrmsmask = "(:1-37)",
/
&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
"Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 428 826 827
Note: This is usually a symptom of some deeper
problem with the energetics of the system."
Have attached the out file too!
Please suggest where I have gone wrong.
--
Regards,
Pallavi Mohanty
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 27 2015 - 22:30:05 PST
