Dear Amber Community,
I’m using Amber20 and I’m doing input file preparation for constant pH MD simulation. I have a question about the CPHFIRST_SOL atom number in the .cpin file. This input can be used to define the first solvent atom to exclude from the GB calculation in the protonation state evaluation.
For the protonation state evaluation, I want to include a few water molecules in the calculation, but I don’t want any of the ions (because many of the ions might exchange with ions in the bulk solution). However, after I set up the system with the leap program, I found that the ions are always written before the waters. If my understanding is correct, when the CPHFIRST_FIRST atom corresponds to a water molecule to be included in the calculation, the ions will become “included” as well because they appear before the water molecules.
I wonder if there’s a way to customize the solvent selection or to “deselect” the ions. Thank you for your kind advice in advance!
Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu
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Received on Sat Jul 24 2021 - 23:30:03 PDT
