An extension of earlier problem in generation of prmtop and inpcrd files follows here. After a long time I had to use xleap to generate parameter and coordinate files for a system comprising of an organic molecule, protonated methanol and Cl atom. Now, organic molecule is not an issue. antechamber tutorial clearly explains how to do that. So, any organic molecule like MEOH is also not a problem. But MEOH2 could be. I have written about how to deal with systems like MEOH2 or extra protonated oxygen systems. But if you want to bring an organic molecule, protonated methanol(MEOH2) and Cl atom together and create parameter and coordinate file for that, it may not be as easy as it appear. Since I had lost touch with xleap for sometime, I totally forgot the small tricks I found to work in xleap. I started working with: * the separate pdb files for each molecular unit. * then create a single pdb file using packmol for the whole system. * create prepin or mol2 file corresponding to combined p
Find some interesting facts,methods, basics in Computational Chemistry