Hi,
You need to define the protonation sate vie pdb2gmx.
pdb2gmx -tyr -lys
On 27/09/10 2:34 PM, sonali dhindwal wrote:
Hello All,
I came through this research article, in which author has selectively
deprotonated and protonated some of the residues to simulate the
condition for electrostatic interaction with the substrate while
carrying out molecular dynamics simulation.
It will be appreciable, if you could help me regarding the same, how
to deprotonate Tyr and Ser residue and protonate Lysine residue of the
protein while preparing the protein topology to be used for molecular
dynamics simulation in Gromacs.
Thanks and Regards.
--
Sonali Dhindwal
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