I've tried using the H++ server to generate protonated states of Acetylcholinesterase (pdb ID = 1GQR). But every time I try to load the generated file into AMBER (used pdb4amber) , I seem to get an error. Visual inspection of the pdb file seems to yield no insight into the problem.
Is there any other method I could predict the protonated state of the molecule at a particular pH?
Hi Mohomed,
I recommend PDB2PQR server:
http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/
Hi Mohomed, take a look at the ProteinPrepare web application (www.playmolecule.org). Its uses PROPKA3.1 for protonation prediction plus PDB2PQR for H-bond network optimization. You can then download results and optimized structure for simulation.
Gerard Martinez It is really great and user-friendly. I used it but I had a tiny problem. I cant change the calculated state of Histidine to what I want. I change the state but after downloading the pdb it is the same as calculated (not what I choose)
Hi Mohomed Afnan
It's been 3 years since you asked but I'll leave this answer here for anyone who comes across this problem.
The PDB output from H++ is not compatible with AMBER, and for that reason you should use ambpdb to generate your PDB structure from H++ topology and coordinate files.
e.g. ambpdb -p 0.15_80_10_pH6.5_1OKL.top -c 0.15_80_10_pH6.5_1OKL.crd > 1OKL_Hpp.pdb
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