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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 07 2017 - 03:00:03 PST
