Dear Amber users,
I would like to make clear how a constant pH simulation in explicit solvent
is performed:
1. ASP, GLU and HIS are renamed into AS4, GL4 and HIP in the pdb file.
2. tleap is opened, leaprc.constph and the pdb are loaded off.
3. The system is neutralized/necessary ions are added and solvated (SPC/E,
OPC, etc).
4. prmtop and inpcrd file are saved.
5. prmtop file with the new radii is obtained employing cpinutil.py
6. The system is minimized and heated (PBC).
7. The system is equilibrated (NPT) and the production run is started.
Is icnstph=2 option introduced with the beginning of NPT equilibration or
at which stage?
Thank you in advance,
Nick
Nikolay Kuzmich
Department of Drug Safety,
Research Institute of Influenza,
WHO National Influenza Centre of Russia,
15/17 Professor Popov St.,
Saint-Petersburg
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Received on Wed Aug 01 2018 - 03:00:03 PDT
