I am running MD simulations at various pH using GROMACS. I used PDB file generated by H++ server. I want a good quality image of titration curve. please suggest if any softwares available?
You're not going to get any information about titration from MD simulations with static topologies. Constant pH methods may be useful, but these are not standard within Gromacs, though people have modified the software and published their results IIRC.
I just wanted to plot a graph like figure 1 and table 1 as mentioned in the attached paper. Please have a look. Thanks
As I said, you cannot obtain such plots from simple MD. To do such simulations, as you will note from the Methods, the authors have used custom software to do constant-pH MD. I would suggest contacting the corresponding author to request the custom code; you cannot do this with standard Gromacs software.
Hi Faez,
Amber14 provides code for constant pH simulations both in implicit and explicit solvent. There is also a program, cphstats, for post simulation analysis of protonation states. Since you've already performed your simulations, this may not be helpful but maybe you can get some ideas from that code on how to proceed. Check out Chapter 22 of the Amber14 manual.
Pawel
Thanks Pawel,
I used "pKa calculation and protein ionization" module present in Discovery Studio 4.0. The results are perfect at every pH values.
Thanks
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