[gmx-users] How Gromacs differentiate same atom pairs and bond length having different charges from info in Pdb files? For example

Justin Lemkul jalemkul at vt.edu
Sun Oct 29 14:36:44 CET 2017

On 10/29/17 1:27 AM, 묵타친모이바삭 wrote:
> For example in this paper OH of carboxyl group and Phenolic OH group 
> has same atoms and bond length but slightly different charges.
> But How the gromacs will differentiate from the datas it gets Pdb file?
> Assuming pdb file contains only coordinates of different atoms.

PDB files contain atom and residue names, not just coordinates. The 
residues tell pdb2gmx how to construct things, and parameters are 
assigned to each atom based on its name.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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