[AMBER] Setting up a pdb file for a QM/MM calculation with explicit water

From: Corum, Katharine W <katharine-corum.uiowa.edu>
Date: Mon, 8 Aug 2016 21:33:12 +0000

Hi Everyone,

I am new to Amber and my ultimate goal is to run a QM/MM calculation with explicit water molecules. I am staring from a pdb file that contains a small protein (46 residues) and 2 water molecules. Then I will work my way up to my actual protein of interest.

When I use the command:

$AMBERHOME/bin/pdb4amber -i original.pdb -o new.pdb --reduce

My water molecule oxygen atoms do not get H atoms placed on them. I can use another program to add H but when I use tleap to generate the name.prmtop and name.inpcrd files I run into issues when explicit water molecules are present. I would like my 2 water molecules in addition to using the solvatebox command to solvate my protein.

Thanks for any help! Or if you have any tips/tutorials for running QM/MM calculations that would be greatly appreciated.

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Received on Mon Aug 08 2016 - 15:00:03 PDT
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