Hi. I have some problems using ff_charmm27 ported in gromacs 4.5.3. 1) I want to build a topology of phosphorylated tyrosine in one position of activated protein. I can make it with swissparam.ch server (getting .itp) or by my hands. But the situation is complicated enough for me, because of necessity to add some hydrogenes (to ester O in phosphate group) to the structure from Marvel Sketch. In other case server claimed the mol2 file is bad. So what to do? Add hydrogens to this oxygenes or not? I'm not sure it is right... I think they must be 'free' from H... 2) I need to include several .itp (tyrosine-PO3 and ligand). Adding strings "include..." before [molecule] section in the top of .top file. And when I did grompp i've got an error invalid order [atomtype] for the last itp. It isn't important which .itp is first, cause the exchange of the strings order do nothing: just an error for the 'new' last .itp
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