It is likely that you have some groups which are not covered by "Protein" and "Other". You can use "Protein" and "Non-Protein" in stead. But make sure that the two groups correspond to two distinct groups in your system. You may run into trouble if you have some non-standard residue in your protein which will end up in the "Non-Protein" group.
Cheers,
Tsjerk
Dear all;
I am trying to calculate the binding free energy of an MHC-molecule and a peptide by thermodynamic integration method. The system contains binding domain of MHC molecule, a peptide presented on it, water-molecules (about 13,000), and ions (Na+ and Cl- at PBS-concentration).
After energy minimization, I tried to equilibrate the system with the mdp-file as follows, and an error-message appeared as such;
"Fatal error.
Not enough ref_t and tau_t values."
How should I change the conditions ?
Many thanks for your help.
cpp = /lib/cpp
define =
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 100000
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 10000
nstenergy = 250
nstxtcout = 10000
xtc_precision = 1000
xtc_grps = Protein
energygrps = Protein other
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 0.9
coulombtype = Reaction-Field
epsilon_r = 78.0
rcoulomb = 1.4
vdw-type = Cut-off
rvdw = 1.4
tcoupl = Berendsen
tc-grps = Protein other
ref_t = 300 300
tau_t = 0.1 0.1
pcoupl = Berendsen
tau_p = 1.0
compressibility = 4.6e-5
ref_p = 1.0
gen-vel = yes
gen-temp = 300
gen-seed = $RANDOM
constraints = all-bonds
Hiromichi Tsurui MD, PhD
Dept. Pathology,
Juntendo University
Phone:81-3-5802-1039
Fax:81-3-3813-3164
[EMAIL PROTECTED]
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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