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

From: David A Case <>
Date: Tue, 9 Aug 2016 15:30:04 -0400

On Tue, Aug 09, 2016, Corum, Katharine W wrote:
> 3. Next I use tleap: $AMBERHOME/bin/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB

This shows the advantage of telling the list exactly what you did: the above
command is no longer sufficient, since it loads *only* protein libraries.
You also need a command like "source leaprc.water.tip3p" (choose you desired
water model).

> Unknown residue: HOH number: 46 type: Terminal/beginning

This is a result of not loading any water libraries.


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Received on Tue Aug 09 2016 - 13:00:02 PDT
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