[gmx-users] Respect waters in crystallographic pdb file?

[Justin Lemkul]

On 8/20/15 10:06 AM, Jorge Fernandez de Cossio Diaz wrote:
> And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command:
>
> genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL <<<"SOL"
>
> Is there a chance that this replaces one of the original crytallographic waters with the CL?
>

There's always a chance; it's random.

It's easy to check and if you get an undesired result, just change the value of 
-seed.  Or distinguish the crystal waters as some other [moleculetype] name, 
which requires some topology hacking.

-Justin

> Thanks. Best,
> cossio
>
> ------------------------------
>
> Message: 2
> Date: Mon, 17 Aug 2015 14:14:28 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Respect waters in crystallographic pdb file?
> Message-ID: <55D22484.9030705 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> They should be in the same place they always were (unless you've modified the
> box dimensions, in which case the coordinates of everything get changed).  But
> genbox shouldn't delete waters that were already present.  The crystallographic
> waters should always be the first ones written after e.g. the protein.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote:
>> Hi all, I have a crystallographic PDB file which comes some waters molecules.
>> I want to run an MD simulation which includes those water molecules. After
>> generating the topology file (which includes the waters) and defining the box
>> shape, I fill the box with solvent using genbox. At this point it becomes
>> impossible to track down visually where the water molecules are. My question
>> is if the file that genbox outputs still contains the crystallographic water
>> molecules? Or are they replaced by the molecules added by genbox? Thanks in
>
> ---------------------------------------------------
>
> [http://5.cim.co.cu/cim.gif]
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================