We report the implementation of an all-atom Brownian dynamics simulation mo
del of peptides using the constraint algorithm LINCS. The algorithm has bee
n added as a part of UHBD. It uses adaptive time steps to achieve a balance
between computational speed and stability. The algorithm was applied to st
udy the effect of phosphorylation on the conformational preference, of the
peptide Gly-Ser-Ser-Ser. We find that the middle serine residue experiences
considerable conformational change from the C-7eq to the alpha (R) structu
re upon phosphorylation. NMR (3)J coupling constants were also computed fro
m the Brownian trajectories using the Karplus equation. The calculated (3)J
results agree reasonably well with experimental data for phosphorylated pe
ptide but less so for doubly charged phosphorylated one.