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

[Justin Lemkul]

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

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