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

From: David A Case <>
Date: Tue, 9 Aug 2016 07:52:06 -0400

On Mon, Aug 08, 2016, Corum, Katharine W wrote:

> 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.

Just saying that you "ran into issues" is not very informative. LEaP
generally has no problem in adding hydrogens to water molecules. There must
be something special about your case that is inhibiting this. But without
knowing exactly what you did, and (more imprortantly) anything about what
problems you might have encountered, people on the list will not be able to
provide much help.


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Received on Tue Aug 09 2016 - 05:00:03 PDT
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