Hello,
Here is an Amber user ;)
But your question is trivial: predict pKa values (e.g. using propka or H++
server) as you always should do.
But with pH=2, you likely should have all Asp, Glu & His protonated, so
just change their names to ASH, GLH and HIP before preparing your
simulation files with tLeap/xLeap.
Marc
On 28 June 2016 at 08:18, Atila Petrosian <atila.petrosian.gmail.com> wrote:
> Dear Gromacs users,
>
> I want to study MD simulation of my protein in an special pH (2).
>
> I want to investigate partially unfolding in this protein.
>
> How to set charge of aminoacids in pdb file, prior to start MD?
>
> Any help will highly appreciated.
>
> Best
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Received on Tue Jun 28 2016 - 01:30:02 PDT
