Hi all, I have added a non standard amino acid 'Hydroxyproline' to my forcefield (from literature) Charmm27 and after using pdb2gmx i could see that the system has a non integer charge value for 1 protein chain out of 3 protein chains. (All 3 chains contain the non standard amino acid) The problem is occuring in the chain in which the terminal residue is this hydroxyproline. (All other places where the 'HYP' residue appears, the charge is 0). I tried using different terminii just to be sure that the problem is not because of the terminii.
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