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

From: Vlad Cojocaru <>
Date: Thu, 7 Dec 2017 11:52:10 +0100

Still problematic if the final PDB has a truncated octahedron box
because one needs to set a box before saving topology and coordinates.
The "setBox" command in leap only sets cubic boxes ... Sure, the
topology and the coordinate files can be then manually edited ....

Alternatively, one could also create an additional Leap library unit for
the water residues with modified residue name and then it should work as
well ...

So, yes, this may work with some manual intervention but still it would
be nice if "addIons" and "addIonsRand" would have an option to define
the solute/solvent from the command syntax.


On 12/07/2017 11:39 AM, Bill Ross wrote:
> 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.
> Bill
> 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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Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Thu Dec 07 2017 - 03:00:05 PST
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