[gmx-users] Non integer charge value

Hemalatha Jayabal hemalathajayabal at gmail.com
Thu May 10 14:29:46 CEST 2018

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.

What should be done in such a case?

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