some questions about water molecules in the trajectory file of GMX and a little warning appeard when amber14sb-OL15 force field was used.

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王宁

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Mar 23, 2020, 9:53:36 AM3/23/20
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Hi everyone, 

     I am a freshman to use g_mmpbsa tool for Protein-ligand binding energy analysis.  One question about the water and salt molecules exist in the trajectory file (*.xtc). Do water and salt molecules matter the final results of binding energy calculation, if so, why the water and salt molecules disappeared in tutorial files.     Another question is about the amber14sb force field application in g_mmpbsa.  I found a strange phenomenon that amber14sb force field could cause these warnings during the g_mmpbsa calculation, but amber99sb-ildn force field doesn't have similar things. 

WARNING: Radius for atomtype "2C" not found. Assigning radius to 1.00 

WARNING: Radius for atomtype "3C" not found. Assigning radius to 1.00 

WARNING: Radius for atomtype "2C" not found. Assigning radius to 1.00 

WARNING: Radius for atomtype "2C" not found. Assigning radius to 1.00 

WARNING: Radius for atomtype "2C" not found. Assigning radius to 1.00 

WARNING: Radius for atomtype "3C" not found. Assigning radius to 1.00 

WARNING: Radius for atomtype "3C" not found. Assigning radius to 1.00 

WARNING: Radius for atomtype "2C" not found. Assigning radius to 1.00




Any suggestions were welcome!

thanks!


wangning
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