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

From: Bill Ross <>
Date: Thu, 7 Dec 2017 02:39:20 -0800

Edit the pdb file and change the residue names of the selected waters,
use addions/rand, savepdb, and change the 'saved' residue names back to WAT.


On 12/7/17 2:35 AM, Vlad Cojocaru wrote:
> Thanks Bill,
> As mentioned in my email, we'd like to avoid using "addIons2" and still
> use "addIons" or "addIonsRand" after solvation and we are wondering
> whether there is a way to avoid replacing selected solvent molecules ...
> If we use addions2 before solvation with large number of ions, we create
> voids in the system and if we use it after solvation, it is terribly
> slow and ions are added out of the box
> Best,
> Vlad
> On 12/07/2017 11:24 AM, Bill Ross wrote:
>> "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?
>> Bill
>> 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 - 03:00:04 PST
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