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I want to generate input files for MD simulation complex having a polypeptide chain, an RNA duplex and Mn2+ ions at pH 7.0 in water. For that first I want to use pdb2pqr server for assigning protonation states of individual entities. The server is giving error and not returning pqr file. It is working fine for only protein chain. So now I came up with an idea that first I should make pqr for only protein chain and then after I should add the coordinates of ligands and RNA. Then that file i should use for input generation in charm gui. Plz give valuable suggestions.