problem in determining atom types and charges for ligand atoms to type in the topology file

From: Mamon Hatmal (hatmal_at_usc.edu)
Date: Thu Aug 29 2013 - 06:03:17 CDT

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Hi NAMD users,

For creating PSF file for a ligand in a protein using VMD, we have to use an input file (topology file) for the ligand (in addition to the topology file of the protein) which contains atom types. My problem is how to determine atom types of that ligand in the topology file, I tried to do it manually but it is tedious and prone to many errors.

Best,

• Next message: Kenno Vanommeslaeghe: "Re: problem in determining atom types and charges for ligand atoms to type in the topology file"
• Previous message: Ana Celia Vila Verde: "how does NAMD calculate intramolecular electrostatic interactions between Drude pairs?"
• Next in thread: Kenno Vanommeslaeghe: "Re: problem in determining atom types and charges for ligand atoms to type in the topology file"
• Reply: Kenno Vanommeslaeghe: "Re: problem in determining atom types and charges for ligand atoms to type in the topology file"
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