  The Cherenkov Telescope Array (CTA) is the future ground-based observatory
for gamma-ray astronomy at very high energies. The atmosphere is an integral
part of every Cherenkov telescope. Different atmospheric conditions, such as
clouds, can reduce the fraction of Cherenkov photons produced in air showers
that reach ground-based telescopes, which may affect the performance. Decreased
sensitivity of the telescopes may lead to misconstructed energies and spectra.
This study presents the impact of various atmospheric conditions on CTA
performance. The atmospheric transmission in a cloudy atmosphere in the
wavelength range from 203 nm to 1000 nm was simulated for different cloud bases
and different optical depths using the MODerate resolution atmospheric
TRANsmission (MODTRAN) code. MODTRAN output files were used as inputs for
generic Monte Carlo simulations. The analysis was performed using the MAGIC
Analysis and Reconstruction Software (MARS) adapted for CTA. As expected, the
effects of clouds are most evident at low energies, near the energy threshold.
Even in the presence of dense clouds, high-energy gamma rays may still trigger
the telescopes if the first interaction occurs lower in the atmosphere, below
the cloud base. A method to analyze very high-energy data obtained in the
presence of clouds is presented. The systematic uncertainties of the method are
evaluated. These studies help to gain more precise knowledge about the CTA
response to cloudy conditions and give insights on how to proceed with data
obtained in such conditions. This may prove crucial for alert-based
observations and time-critical studies of transient phenomena.
