Dear Agnivo
Regarding your inquiry: there is an online tool to determine the pka
value of a protein (of its aminoacids) if you have the pdb file of
your protein
The program is Propka see it at internet ,( See the paper Very
Fast Empirical Prediction and Rationalization of Protein pKa
Dear Users
I am trying to find the net charge at the physiological pH value for a
protein molecule (Thrombin) in my case and am wondering if it is possible
to use GROMACS for doing it.
I am very new to GROMACS and at present I have been going through the
tutorials by Dr. Lemkul. I have seen that
On 9/9/14 3:51 PM, Agnivo Gosai wrote:
Dear Users
I am trying to find the net charge at the physiological pH value for a
protein molecule (Thrombin) in my case and am wondering if it is possible
to use GROMACS for doing it.
I am very new to GROMACS and at present I have been going through
Quick answer is no.
In fact, that's really not what (standard) molecular dynamics is for. You
need a constant-pH MD method for that. Read this to get a bit more
acquainted with the subject (might be overkill for you, because I doubt
this is what you want/need):
