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

From: David A Case <>
Date: Sun, 25 Jul 2021 08:24:03 -0400

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


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Received on Sun Jul 25 2021 - 05:30:02 PDT
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