Re: [AMBER] Include specific solvent in constant pH MD simulation by CPHFIRST_SOL

From: He, Amy <he.1768.buckeyemail.osu.edu> Date: Sun, 25 Jul 2021 13:05:16 +0000

--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu
From: David A Case <dacase.chem.rutgers.edu>
Date: Sunday, July 25, 2021 at 8:24 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Include specific solvent in constant pH MD simulation by CPHFIRST_SOL
On Sun, Jul 25, 2021, He, Amy wrote:
>after I set up the system with the leap program, I found that the ions are
>always written before the waters.
You can use "set default reorder_residues off" in your leap file to prevent
the re-ordering of residues.  Don't worry about the warnings in the manual:
I use this option all the time, and have never seen any problems.
Then, in your input PDB file, put the ions and waters in the order that you
want.
....dac
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