We calculate the atmospheric flux of prompt neutrinos, produced in decays of the charmed particles at energies beyond 1 TeV. Cross sections of the $D$-mesons and ${Lambda}^{+}_{c}$ baryons production in pA and $pi$A collisions are calculated in the phenomenological quark-gluon string model (QGSM) which is updated using of the recent measurements of cross sections of the charmed meson production in the LHC experiments. A new estimate of the prompt atmospheric neutrino flux is obtained and compared with the limit of the IceCube experiment as well as with predictions of other charm production models.