Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions

From: Bill Ross <>
Date: Thu, 7 Dec 2017 02:24:31 -0800

"The second approach implemented by the command "/addions2/" does almost
the same thing as "addions" except that it treats solvent molecules the
same as solute."

Sounds like what you want?


On 12/7/17 2:14 AM, Vlad Cojocaru wrote:
> Dear Ambers,
> This may be a rather trivial question but somehow the following issue is
> not clear to me. The issue came up because recently, we had to load in
> Leap structures that have already a large number of water molecules that
> we'd like to exclude from being replaced by ions during the leap
> procedures to add ions.
> When using "addIons" or "addIonsRand", solvent molecules overlapping
> with future ions positions are removed (replaced with ions). Now, if we
> have a structure with a layer of solvent molecules that we want to keep,
> how do we instruct the addions command to not replace those specific
> solvent molecules ? If the PDB file with waters is loaded as a unit in
> leap, will the entire unit be considered "solute" or will the waters in
> the unit be labeled automatically as "solvent" ?
> We know "addions2" does not replace solvent molecules and could be used
> prior to solvation but still we would like to use "addions" or
> "addIonsRand" after solvation ...
> Thanks for clarifying this
> Best wishes
> Vlad

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Received on Thu Dec 07 2017 - 02:30:02 PST
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