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

From: Ayesha Fatima <>
Date: Tue, 9 Aug 2016 07:36:48 +0800

Hi Kate. The tutorial is already available on the amber website to prepare
the molecule for QM/MM. Following can help solve a few general issues.
Regarding the tips, I think the one that worked for me was preparing my
molecule in the regular way using tleap. the ligand was charged RESP
server. After minimisation and equilibration in the general way for MD,
then the switch to QM/MM can be done using the QM commands in the md
production file.
I hope it helps.

On Tue, Aug 9, 2016 at 5:33 AM, Corum, Katharine W <> wrote:

> 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.
> Katie
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Received on Mon Aug 08 2016 - 17:00:03 PDT
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