Dear All,
I am following this particular tutorial to calculate free energy of binding : http://ambermd.org/tutorials/advanced/tutorial24/
My question is as follows:
Some of the molecules are charged, hence I have made a file (charge.txt) mentioning the total charges and spin multiplicity. But the ones that are not charged, I did not mention anything.
I still get this error message when I am generating parameter files :
WARNING: The ligand mol2 file /home/local/soemya-loc/site_1_WT/structs/Lig_ZINC18279893.mol2 contains charges. If you conduct a charge
calculation this can result in additional warning messages. To avoid this,
please use only ligand mol2 files with zero atomic charges as input.
This particular molecule is neutral (Lig_ZINC18279893).
If a molecule has positively and negatively charged atoms but an overall charge of zero, should I still mention this in the charge information file (charge.txt)?
I look forward for your suggestions.
Thanks
Regards
Sowmya
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Received on Fri Mar 17 2017 - 08:30:02 PDT
