Dear Erik you said Amber03 was not parameterized with charge groups and last column in your rtp entry holds the chargegroup numbers. but cgnr column in my top file does not looks just like it. in case of H1, H2 and H3.
* H1 amber99_17 0.16420 2 ** H2 amber99_17 0.16420 3 ** H3 amber99_17 0.16420 4 ** ** *. that's ok. but why *and my top file is as follow : ** ** ** nr type resnr residue atom cgnr charge mass ** **2 amber99_17 1 NGLY H1 2 0.1642 1.008 ** 3 amber99_17 1 NGLY H2 2 0.1642 1.008 ** 4 amber99_17 1 NGLY H3 2 0.1642 1.008 ** * thanks for your attention
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