Re: Residue Charges

From: Sharp, Kim (sharpk_at_pennmedicine.upenn.edu)
Date: Fri Mar 02 2018 - 08:49:05 CST

the charge on each atom is specified in the topology file(s) that you
used to build the system- they are stored in the *.psf file, and they do
not change during the simulation, which is why they don't need to be
written to the dcd file.

On 03/02/2018 09:35 AM, Alex Saad-Falcon wrote:
> In each frame of a .dcd file, the positions of all the atoms are
> available. I would also like to know the formal charge each atom has.
> Online, it is possible to find typical charges for residues under
> certain conditions such as pH. However, it would be better to pull the
> charge of each residue from NAMD somehow. Does anyone know how?
>
> Thanks,
>
> Alex

-- 
Kim Sharp, Ph.D,
Dept. of Biochemistry & Biophysics
Chair, Biochemistry & Molecular Biophysics Graduate Group
Perelman School of Medicine at the University of Pennsylvania
805A Stellar Chance
Philadelphia, PA 19104
webpage: crystal.med.upenn.edu
215-573-3506

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